From jstroud at mbi.ucla.edu Tue Mar 1 22:06:12 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Tue, 1 Mar 2005 19:06:12 -0800 Subject: [BiO BB] SGD<==>Swissprot Message-ID: <200503011906.12920.jstroud@mbi.ucla.edu> I'm looking for the quickest way to go back and forth between SGD and Swissprot. The SGD website suggests this is easy, but its not obvious how to go about it. Thank you for any help. James -- James Stroud, Ph.D. UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 From nuraini at cs.usm.my Tue Mar 1 22:05:27 2005 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Wed, 2 Mar 2005 11:05:27 +0800 Subject: [BiO BB] Z-score and E-value. Message-ID: <005b01c51ed4$b65b1650$4482cf0a@MyBox2> Hi all, I am reading the Protein Sequence Comparison and Protein Evolution tutorial ISMB2000 by William R. Pearson, on Page 13 Table 3 it list down searchhing the database with human ATP-ase, high scoring sequences. I can figure out how SW was done, but I cannot understand how to calculate z-score and E and percentage. XCan anyone guide me of how to get material or examples or books or website where it show detail example how to get those value starting from the input value to output value.. Thanks a lot.. I have no statistic background and though I got some notes on how to calculate z-score but this is different. Nur'Aini binti Abdul Rashid Pusat Pengajian Sains Komputer Universiti Sains Malaysia Pulau Pinang. -------------- next part -------------- An HTML attachment was scrubbed... URL: From idoerg at burnham.org Wed Mar 2 01:29:27 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 1 Mar 2005 22:29:27 -0800 Subject: [BiO BB] Z-score and E-value. In-Reply-To: <005b01c51ed4$b65b1650$4482cf0a@MyBox2> Message-ID: Judging from your questions, you should probably fortify your statistical background. However, to answer your questions specifically, the exact calculations are described later on in the tutorial, pages 30 onwards. Best, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo ------------------------------------- Automated Protein Function Prediction Meeting, June 24, 2005 http://ffas.burnham.org/AFP On Wed, 2 Mar 2005, Nur'Aini Abdul Rashid wrote: > Hi all, > > I am reading the Protein Sequence Comparison and Protein Evolution > tutorial ISMB2000 by William R. Pearson, on Page 13 Table 3 it list > down searchhing the database with human ATP-ase, high scoring > sequences. I can figure out how SW was done, but I cannot understand > how to calculate z-score and E and percentage. XCan anyone guide me of > how to get material or examples or books or website where it show > detail example how to get those value starting from the input value to > output value.. > > Thanks a lot.. I have no statistic background and though I got some > notes on how to calculate z-score but this is different. > > Nur'Aini binti Abdul Rashid > Pusat Pengajian Sains Komputer > Universiti Sains Malaysia > Pulau Pinang. From smagarwal at yahoo.com Thu Mar 3 03:03:31 2005 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Thu, 3 Mar 2005 08:03:31 +0000 (GMT) Subject: [BiO BB] Generate Quaternary structure of protein from monomer Message-ID: <20050303080331.90307.qmail@web13626.mail.yahoo.com> Hi all I would like to know that how to generate Quaternary structure of protein from monomer pdb file. Is there any script avaliable for the same. Thanks Subhash ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony From dmb at mrc-dunn.cam.ac.uk Thu Mar 3 04:16:37 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 3 Mar 2005 09:16:37 +0000 (GMT) Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <20050303080331.90307.qmail@web13626.mail.yahoo.com> Message-ID: On Thu, 3 Mar 2005, Subhash Agarwal wrote: >Hi all > >I would like to know that how to generate Quaternary >structure of protein from monomer pdb file. Is there >any script avaliable for the same. Best use http://www.ebi.ac.uk/msd/ Go here with your pdb code http://pqs.ebi.ac.uk/pqs-quick.html > >Thanks >Subhash > >________________________________________________________________________ >Yahoo! India Matrimony: Find your life partner online >Go to: http://yahoo.shaadi.com/india-matrimony >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From val at vtek.com Thu Mar 3 09:06:16 2005 From: val at vtek.com (val) Date: Thu, 3 Mar 2005 09:06:16 -0500 Subject: [BiO BB] Generate Quaternary structure of protein from monomer References: Message-ID: <085e01c51ffa$2b1245b0$c400a8c0@sony> Are you serious? Is there 'a script' in this world to reconstruct a quaternary protein structure based on primary (monomer) one? That would be too good... Val ----- Original Message ----- From: "Dan Bolser" To: "The general forum at Bioinformatics.Org" Sent: Thursday, March 03, 2005 4:16 AM Subject: Re: [BiO BB] Generate Quaternary structure of protein from monomer > On Thu, 3 Mar 2005, Subhash Agarwal wrote: > > >Hi all > > > >I would like to know that how to generate Quaternary > >structure of protein from monomer pdb file. Is there > >any script avaliable for the same. > > Best use http://www.ebi.ac.uk/msd/ > > Go here with your pdb code http://pqs.ebi.ac.uk/pqs-quick.html > > > > >Thanks > >Subhash > > > >________________________________________________________________________ > >Yahoo! India Matrimony: Find your life partner online > >Go to: http://yahoo.shaadi.com/india-matrimony > >_______________________________________________ > >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From willy_valdivia at orionbiosciences.com Wed Mar 2 02:53:09 2005 From: willy_valdivia at orionbiosciences.com (willy_valdivia at orionbiosciences.com) Date: Wed, 2 Mar 2005 00:53:09 -0700 Subject: [BiO BB] Fifth Virtual Conference on Genomics and Bioinformatics Message-ID: <20050302075309.21126.qmail@webmail12.prod.mesa1.secureserver.net> Dear members of the list: Please apologize multiple postings of the following message: Fifth Virtual Conference on Genomics and Bioinformatics (October 25-28, 2005) Main Location: Arlington Virginia USA http://www.virtualgenomics.org/vcgb/conference_2005.htm No Registration Fees Objectives: * Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. * Address the benefits and limitations of the newest developments in post-genomic technologies. * Explore the social and ethical implications of genomic and bioinformatic research. * Establish new ways to introduce the high school community to today's multidisciplinary science. Paper Submission Deadline: June 30, 2005* Accepted Manuscripts will be invited for oral presentations, published in the Virtual Conference Proceedings and considered in PLoS Computational Biology Questions: information at virtualgenomics.org Program Co-Chairs and Review Committee Willy Valdivia-Granda (Founder VCGB), Orion Integrated Biosciences, Inc. USA Kim Baldrigde, Universit?t Z?rich, Switzerland Eric Davison, California Institute of Technology. USA Krishan Arora, National Institutes of Health. USA Greg Cardinale, Sandia National Laboratory, USA Steven F. Jennings, University of Arkansas, Little Rock. USA Maricel Kann, National Institutes of Health. USA Sarah Tegen, National Academy of Sciences. USA Joaquin Dopazo, Spanish National Cancer Center. Spain Inna Dubchak, Lawrence Berkeley National Laboratory. USA Keith Dunker, University of Indiana. USA Kevin Karplus, University of California, Santa Cruz. USA Phillip Lord, University of Manchester. UK Anna Panchenko, NCBI, NLM, National Institutes of Health. USA Teresa Przytycka, NCBI, NLM, National Institutes of Health. USA Amit Sheth, University of Georgia. USA Robert Stevens, University of Manchester. UK Deanne Taylor, Serono Reproductive Institute. USA Alfonso Valencia, Centro Nacional de Biotecnologia. Spain Access Grid and Technical Co-Chairs Tom Coffin, Access DC, USA Michael J. McMahon Jr., University of Nevada Reno. USA Brian Gleason. InSors, Inc. USA From rajalogan at hotmail.com Wed Mar 2 11:22:32 2005 From: rajalogan at hotmail.com (Raja Loganantharaj) Date: Wed, 2 Mar 2005 10:22:32 -0600 Subject: [BiO BB] Announcing 2nd Annual Bioinformatics Symposium in Lafayette on April 18, 2005 In-Reply-To: <005b01c51ed4$b65b1650$4482cf0a@MyBox2> Message-ID: Place: Lafayette, Louisiana Date: April 18, 2005 Paper due: March 18, 2005 Symposium web site: http://www.cacs.louisiana.edu/bioinformatics/symp05/index.html You are invited to submit a paper to the Second Annual Bioinformatics Symposium 2005. The symposium's goal is to build a bridge among the researchers working in industries, academic and research institutions. This forum will provide an opportunity to learn and to understand the ongoing research activities that may help spark some new collaboration for future research and funding opportunities in this area. Those who are working in the area of molecular biology, computer science, and statistics are encouraged to participate in the symposium to acquaint with the current research agenda of Bioinformatics and to be informed about potential funding sources. Accepted papers will be scheduled for a short podium presentations, and will be published in the conference proceedings. Please submit a complete paper or an extended abstract up to 5 pages. Computer science papers must show biological relevance, and biology papers must stress the computational contribution to the results. Topics of interest include, but are not limited to: Sequence alignment Gene discovery Protein structure prediction Protein to protein interaction RNA structure prediction Evolutionary phylogenetic tree Application of machine learning to Bioinformatics Molecular structure and interaction Micro-array analysis Promoter detection algorithms Gene expression Keynote Speakers We are making arrangements to bring renowned researchers and scientists from academic and research institutions and from funding agencies. The keynote speakers will include: Professor Philip E. Bourne Professor of Pharmacology, UCSD Co-Director Protein Data Bank, SDSC Editor-in-Chief PLoS Computational Biology Dr. Fern Y. Hunt Mathematical and Computational Sciences Division National Institute of Standards and Technology (NIST) Participation: Registration is required to attend the symposium. On line registration is opened while seats are available. Thank you for your time -------------- next part -------------- An HTML attachment was scrubbed... URL: From jstroud at mbi.ucla.edu Thu Mar 3 13:38:34 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Thu, 3 Mar 2005 10:38:34 -0800 Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <20050303080331.90307.qmail@web13626.mail.yahoo.com> References: <20050303080331.90307.qmail@web13626.mail.yahoo.com> Message-ID: <200503031038.34765.jstroud@mbi.ucla.edu> Do you know the transformation(s) that relate(s) the protomer to the copies? On Thursday 03 March 2005 12:03 am, Subhash Agarwal wrote: > Hi all > > I would like to know that how to generate Quaternary > structure of protein from monomer pdb file. Is there > any script avaliable for the same. > > Thanks > Subhash > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- James Stroud, Ph.D. UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 From smagarwal at yahoo.com Thu Mar 3 22:25:05 2005 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Fri, 4 Mar 2005 03:25:05 +0000 (GMT) Subject: [BiO BB] Generate Quaternary structure of protein from monomer Message-ID: <20050304032505.46729.qmail@web31501.mail.mud.yahoo.com> Hi all Reply to Dan Bosler answer I knew of these sites and visited them again after u referred. These sites are useful if u have a pdb code avaliable. In my case i have built a homology model for which i need to generate quaternary structure. Reply to James Strond answer Yes, for template structure has a quaternary structure and therefore are known. My Query: How can i use these transformations for generating Quaternary structure? Moreover from the pdb of the template i also need to understand that the transformation are in regard to which monomer. How can i know that. ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony From jstroud at mbi.ucla.edu Thu Mar 3 23:16:29 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Thu, 3 Mar 2005 20:16:29 -0800 Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <20050304032505.46729.qmail@web31501.mail.mud.yahoo.com> References: <20050304032505.46729.qmail@web31501.mail.mud.yahoo.com> Message-ID: <200503032016.29412.jstroud@mbi.ucla.edu> Hi Subhash, You will need to get the transformation matrices from the template. This can be done in the program O < http://www.bioxray.dk/~mok/o-files.html >. The commands you will need are: pdb_read (to read your pdb-file) lsq_explicit (to determine the transformation matrix and store it) The o manual is at < http://www.bioxray.dk/~mok/o/o_man/manual.html > Once you have the transformation stored in the o database (".lsq_rt_?????", where "?????" is the name you provide to the lsq-expl command), you can load your protomer with pdb_read Then you can read in the second copy, again with "pdb_read". Apply the transformation matrix from the template to the second copy with lsq_mol You can read in further monomers and apply the transformation matrix N times until you fill your polymer. You should then write out every monomer with pdb-write and join the files with a text editor, taking care to remove headers and "END" statements between files. Things to think about: (1) Molecule names in O are the first 5 characters only (this can cause serious confusion to first-timers.) (2) If you have a cyclic N-mer where (N > 2) and (N mod 2 = 0) [i.e. even and greater than 2], then you should take care to choose the right two monomers from the template polymer to generate the transformation matrix or you will skip monomers in your model (think about starting at one vertex of a hexagon and transforming 120 degrees versus 60 degrees, etc.--both relate equivalent vertices but the former skips three under all transformations). James On Thursday 03 March 2005 07:25 pm, Subhash Agarwal wrote: > Hi all > > Reply to Dan Bosler answer > > I knew of these sites and visited them again after u > referred. These sites are useful if u have a pdb code > avaliable. In my case i have built a homology model > for which i need to generate quaternary structure. > > Reply to James Strond answer > > Yes, for template structure has a quaternary structure > and therefore are known. > > My Query: > > How can i use these transformations for generating > Quaternary structure? Moreover from the pdb of the > template i also need to understand that the > transformation are in regard to which monomer. How can > i know that. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- James Stroud, Ph.D. UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 From boris.steipe at utoronto.ca Fri Mar 4 00:12:08 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Fri, 4 Mar 2005 00:12:08 -0500 Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <200503032016.29412.jstroud@mbi.ucla.edu> Message-ID: Depending on the crystal symmetry and the orientation of the monomer in the asymmetric unit, this all can be nontrivial. Consider a dimer "()" in a crystal lattice ...()()()()()()... The asymmetric unit contains the monomer "(" or its rotated copy ")" but, depending on where the monomer is located in the unit cell, applying the symmetry matrix once may give you "()" or it may give you ")(". So in order to cover all cases, you may have to apply the matrix to two copies and _translate_ one by one unit cell to give ")()", then decide which of the pairs is the one you want. Pragmatically, and depending how familiar you are with "O" or other crystallography tools, it may be faster downloading the biological unit from PDB or EBI-PQS and then using a superposition tool or Web service to superimpose your model on each of the monomers. It really depends on the spacegroup. Also, depending on the graphics program you use, you may either have to give each of the monomers a separate chain identifier "A", "B", "C" ... (check the biological unit file to see how this is done) or put a "MODEL 1", "MODEL 2" etc. line before each copy and an "ENDMDL" line after it (check any NMR structure ensemble to see how that is used). Hope this helps, Boris On Thursday, Mar 3, 2005, at 23:16 Canada/Eastern, James Stroud wrote: > Hi Subhash, > > You will need to get the transformation matrices from the template. > This can > be done in the program O < http://www.bioxray.dk/~mok/o-files.html >. > > The commands you will need are: > > pdb_read (to read your pdb-file) > lsq_explicit (to determine the transformation matrix and store it) > > The o manual is at < http://www.bioxray.dk/~mok/o/o_man/manual.html > > > Once you have the transformation stored in the o database > (".lsq_rt_?????", > where "?????" is the name you provide to the lsq-expl command), you > can load > your protomer with > > pdb_read > > Then you can read in the second copy, again with "pdb_read". > > Apply the transformation matrix from the template to the second copy > with > > lsq_mol > > You can read in further monomers and apply the transformation matrix N > times > until you fill your polymer. > > You should then write out every monomer with > > pdb-write > > and join the files with a text editor, taking care to remove headers > and "END" > statements between files. > > > Things to think about: > > (1) Molecule names in O are the first 5 characters only (this can cause > serious confusion to first-timers.) > (2) If you have a cyclic N-mer where (N > 2) and (N mod 2 = 0) [i.e. > even and > greater than 2], then you should take care to choose the right two > monomers > from the template polymer to generate the transformation matrix or you > will > skip monomers in your model (think about starting at one vertex of a > hexagon > and transforming 120 degrees versus 60 degrees, etc.--both relate > equivalent > vertices but the former skips three under all transformations). > > > James > > > On Thursday 03 March 2005 07:25 pm, Subhash Agarwal wrote: >> Hi all >> >> Reply to Dan Bosler answer >> >> I knew of these sites and visited them again after u >> referred. These sites are useful if u have a pdb code >> avaliable. In my case i have built a homology model >> for which i need to generate quaternary structure. >> >> Reply to James Strond answer >> >> Yes, for template structure has a quaternary structure >> and therefore are known. >> >> My Query: >> >> How can i use these transformations for generating >> Quaternary structure? Moreover from the pdb of the >> template i also need to understand that the >> transformation are in regard to which monomer. How can >> i know that. >> >> ______________________________________________________________________ >> __ >> Yahoo! India Matrimony: Find your life partner online >> Go to: http://yahoo.shaadi.com/india-matrimony >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- > James Stroud, Ph.D. > UCLA-DOE Institute for Genomics and Proteomics > Box 951570 > Los Angeles, CA 90095 > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From nchandra at physics.iisc.ernet.in Fri Mar 4 01:07:47 2005 From: nchandra at physics.iisc.ernet.in (Dr.Nagasuma Chandra) Date: Fri, 4 Mar 2005 11:37:47 +0530 (IST) Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <20050304032505.46729.qmail@web31501.mail.mud.yahoo.com> Message-ID: Hi Subhash First of all, you need to be sure that your model will have the same quaternary arrangement as your template. There are a number of examples, where diversity is observed in quaternary structure even when subunit structures (and their sequences) show high similarity (>50-70%). Plant lectins are a classic example. If you are sure of the type of quaternary association, either from biochemical data and/or structural analysis of your model and its comparison to the template, it is relatively simple to apply the translational and rotational matrices to obtain a multimer. Hope this helps Nagasuma Chandra *********************************************** Dr. Nagasuma Chandra Bioinformatics centre Indian Institute of Science Bangalore 560 012 Tel: +91-80-22932469 or 23601409 Fax: +91-80-23600551 e-mail: nchandra at physics.iisc.ernet.in *********************************************** On Fri, 4 Mar 2005, Subhash Agarwal wrote: > Hi all > > Reply to Dan Bosler answer > > I knew of these sites and visited them again after u > referred. These sites are useful if u have a pdb code > avaliable. In my case i have built a homology model > for which i need to generate quaternary structure. > > Reply to James Strond answer > > Yes, for template structure has a quaternary structure > and therefore are known. > > My Query: > > How can i use these transformations for generating > Quaternary structure? Moreover from the pdb of the > template i also need to understand that the > transformation are in regard to which monomer. How can > i know that. > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From sgerson at stanfordalumni.org Fri Mar 4 01:26:06 2005 From: sgerson at stanfordalumni.org (Stephanie Gerson) Date: Thu, 03 Mar 2005 22:26:06 -0800 Subject: [BiO BB] Biomimicry in Database Design Message-ID: <088JcDgAg9200S16.1109917566@uwdvg016.cms.usa.net> hello, ?? My name is Stephanie and I'm working with a team to develop a database of ecological relationships.? We are in the process of deciding how the informational content will be stored and organized.? We are interested in how nature stores and organizes information, so to speak, so that we may mimic these methods in our own database design - which is why I'm turning to Bioinformatics.? Is there a branch of Bioinformatics specifically dealing with this question and seeking to model the database after its informational content (i.e. modeling the database after how DNA stores information)?? And if so, can you please direct me to the appropriate resources? ????????? Thank you, ??????????????? *Stephanie +++++++++++++++ Stephanie Gerson sgerson at stanfordalumni.org (c) 415.871.5683 ____________________________________________________________________ From smagarwal at yahoo.com Fri Mar 4 03:25:16 2005 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Fri, 4 Mar 2005 08:25:16 +0000 (GMT) Subject: [BiO BB] Generate Quaternary structure of protein from monomer Message-ID: <20050304082516.57106.qmail@web31506.mail.mud.yahoo.com> Hi all As James and Boris have written that the solution they are able to provide depends on the knowledge of the user with regards to progam O and understanding of crystallography. So i would like to say that neither i have used program O before nor i am cryatallographer. So making things difficult for me. While Dr.Nagasuma Chandra writes that i need to be sure that whether my model has the same quaternary arrangement as my template or not. Sir in this regard i would like to say that the sequence (Query) i have picked for modelling has known function (experimentally characterised) and for the same the template are avaliable and therfore i started working on this protein. My need to generate the quaternary structure is due to reason that i need to observe the active site in the generated model. Also u state that " it is relatively simple to apply the translational and rotational matrices to obtain a multimer". Can u tell me how will u suggest me to do this. Moreover if any of u feels that should mail pdb of generated model and the PDB id of template used, that can also be done by me. Also i am thankful to everybody as u r trying to help me by responding. Please continue to provide support. Thanks Subhash Agarwal ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony From Reichelt at gbf.de Fri Mar 4 04:05:14 2005 From: Reichelt at gbf.de (Joachim Reichelt) Date: Fri, 04 Mar 2005 10:05:14 +0100 Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <20050304082516.57106.qmail@web31506.mail.mud.yahoo.com> References: <20050304082516.57106.qmail@web31506.mail.mud.yahoo.com> Message-ID: <422824CA.9020803@gbf.de> Subhash Agarwal schrieb: >Hi all > >As James and Boris have written that the solution they >are able to provide depends on the knowledge of the >user with regards to progam O and understanding of >crystallography. So i would like to say that neither i >have used program O before nor i am cryatallographer. >So making things difficult for me. > >While Dr.Nagasuma Chandra writes that i need to be >sure that whether my model has the same quaternary >arrangement as my template or not. Sir in this regard >i would like to say that the sequence (Query) i have >picked for modelling has known function >(experimentally characterised) and for the same the >template are avaliable and therfore i started working >on this protein. > >My need to generate the quaternary structure is due to >reason that i need to observe the active site in the >generated model. Also u state that " it is relatively >simple to apply the translational and rotational >matrices to obtain a multimer". Can u tell me how will >u suggest me to do this. > >Moreover if any of u feels that should mail pdb of >generated model and the PDB id of template used, that >can also be done by me. > >Also i am thankful to everybody as u r trying to help >me by responding. Please continue to provide support. > >Thanks >Subhash Agarwal > >________________________________________________________________________ >Yahoo! India Matrimony: Find your life partner online >Go to: http://yahoo.shaadi.com/india-matrimony >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > Perhaps you should try to use BRAGI http://bragi.gbf.de It can create all crystallographic neighbors of a given PDB ID without special knowledge of the user. -- Mit freundlichen Gruessen Best Regards Joachim Reichelt WWW: http://bragi.gbf.de/ _/_/_/ _/_/_/ _/_/_/_/ WWW: http://www.gbf.de/sb _/ _/ _/ _/ _/ WWW: http://www.gbf.de/ _/ _/ _/ _/ _/ _/ _/_/_/ _/_/_/ _/ _/ _/ _/ _/ Mascheroder Weg 1 _/ _/ _/ _/ _/ D-38124 Braunschweig _/_/_/ _/_/_/ _/ Tel: +(49) 531 6181 352 FAX: +(49) 531 2612 388 SB - Strukturbiologie GBF - Gesellschaft fuer Biotechnologische Forschung German Research Centre for Biotechnology See me at: EMAIL: REICHELT at gbf.de WWW: http://www.gbf.de/sb/Reichelt.htm -- Disclaimer -- Standard > Keyword : Opinions, my own, nobody else's, whatsoever ... Man muss sich notfalls jemand mieten, hat man an Geist selbst nichts zu bieten! (Heinz Erhardt) From smagarwal at yahoo.com Sat Mar 5 11:46:58 2005 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Sat, 5 Mar 2005 16:46:58 +0000 (GMT) Subject: [BiO BB] Template selection Message-ID: <20050305164658.29806.qmail@web31510.mail.mud.yahoo.com> Hi all I have a protein (GI:56468480), for which i need to built a homology model. On carrying blast of this protein against PDB sequences, it is revealed that it is probably an protein with calcium binding domain. It ehibits highest similarity to 1DMO. However on viewing the CDD results one is enclined to think that it is frequinin. My question is that is my conclusion right. Should i use 1DMO as template for modelling or a frequnin. Thanks Subhash Agarwal ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony From yvan.strahm at gmail.com Sat Mar 5 13:26:26 2005 From: yvan.strahm at gmail.com (Yvan Strahm) Date: Sat, 5 Mar 2005 10:26:26 -0800 Subject: [BiO BB] Template selection In-Reply-To: <20050305164658.29806.qmail@web31510.mail.mud.yahoo.com> References: <20050305164658.29806.qmail@web31510.mail.mud.yahoo.com> Message-ID: Hi Subhash, You can do a PSI blast using nr as DB and see if after a few round you will fish other sequences wich structure have been determined. Then using swissPDBViewer or modeller, see if you can built a descent model. Does your sequence produce an acceptable model using 1DMO as template? Yvan On Sat, 5 Mar 2005 16:46:58 +0000 (GMT), Subhash Agarwal wrote: > Hi all > > I have a protein (GI:56468480), for which i need to > built a homology model. On carrying blast of this > protein against PDB sequences, it is revealed that it > is probably an protein with calcium binding domain. It > ehibits highest similarity to 1DMO. However on viewing > the CDD results one is enclined to think that it is > frequinin. > > My question is that is my conclusion right. Should i > use 1DMO as template for modelling or a frequnin. > > Thanks > Subhash Agarwal > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From idoerg at burnham.org Sun Mar 6 01:30:11 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat, 5 Mar 2005 22:30:11 -0800 Subject: [BiO BB] Protein Science to have a special section for the AFP SIG Message-ID: The Automated Function Prediction (AFP) meeting organizing committee is happy to announce that Protein Science journal will be publishing a select number of presentations from the AFP in a special section dedicated to the meeting. We urge all the accepted presenters to submit their work as short manuscripts to Protein Science. Submission details will be announced. Note that acceptance of manuscripts to Protein Science is subject to the normal peer-review and editorial decisions. We are very happy that such a distinguished publication is supporting the AFP SIG idea and giving us all a chance to present the results of our discussions to a wider forum. Thus, we are looking forward not only to a very exciting meeting, but to an interesting in-depth analysis of automated function prediction in print. For more infomation on the AFP-SIG, a special interest group meeting of ISMB 2005, please visit: http://ffas.burnham.org/AFP Protein Science journal: http://www.proteinscience.org/ Iddo Friedberg, in the name of the AFP steering committee. -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo ------------------------------------- Automated Protein Function Prediction Meeting, June 24, 2005 http://ffas.burnham.org/AFP From binfoboom at gmail.com Sun Mar 6 12:08:26 2005 From: binfoboom at gmail.com (binfoMatix team) Date: Sun, 6 Mar 2005 22:38:26 +0530 Subject: [BiO BB] binfoPlasma - the bioinformatics encyclopedia is here!!!!! Message-ID: <30a2872c05030609083cf1dba3@mail.gmail.com> Dear Bioinformatics Enthusiast, It brings us immense pleasure to announce the release of binfoPlasma ? the Bioinformatics Encyclopedia (www.binfoplasma.binfomatix.com). On binfoPlasma you can find: 1. Definitions to key terms in bioinformatics and related fields 2. Links to related terms in the encyclopedia 3. Suggested Reading : Links to sources of more information on each term (books, journals, research papers, web sites and other online resources, etc) BinfoPlasma is an online encyclopedia "by the bioinformatics community, for the bioinformatics community". As a binfoPlasman, you can 1. Search binfoPlasma for a specific term definition using the Search/Go option. 2. Browse through subject categories like Mathematics/Life Sciences/Statistics etc for terms. 3. Browse through alphabetical categories for terms 4. Contribute new term definitions to binfoPlasma's growing repository 5. Add more information (text or images) to existing term definitions 6. Share your views on specific topics with other binfoPlasmans through discussions on the "talk pages/user pages". Visit binfoPlasma at www.binfoplasma.binfomatix.com today!!!!! Once again extending a warm invitation to join us on our journey to bioinformatics excellence?.. ~Team binfoPlasma From vidyakothekar at yahoo.com Mon Mar 7 12:51:21 2005 From: vidyakothekar at yahoo.com (vidya kothekar) Date: Mon, 7 Mar 2005 09:51:21 -0800 (PST) Subject: [BiO BB] Generate Quaternary structure of protein from monomer In-Reply-To: <20050304082516.57106.qmail@web31506.mail.mud.yahoo.com> Message-ID: <20050307175121.64738.qmail@web61301.mail.yahoo.com> Dear Subhash I find people are having some confusion regarding crystal packing, and symmetry elements associated with it and multimeric structure of the proteins. Crystal symmetry and packing you can talk if the crystal structure is solved and symmetry groups are observed. Obtaining coordinates of different chains is no problem. There are plenty of programs and tools available with the graphics software or Work stations as O. Even if these are not available, one can write the program very easily and generate the coordinates using PDB coordinates of the monomers using text book level information for the transformation. However, the arrangement of the subunits in the quarternary structure of a protein is a complicated task. It is even more complecated in case of modelled protein or for proteins for which part of the structure is solved. It is true that, if it is not done then it is very difficult to predict the active site. In reality there is no method. The problem is first one should identify constituents of the multimeric structures as same chain, chemically modified chins etc. It is possible to use series of experimental techniques to get tentative guess for protein-protein interaction. Later one can use combination of experiment and theory to arrive at the multimeric structure. In case one has a good template and one is convinced that the modelled proteins and the template for which the X-ray structure is available have the same function and also have same packing, one can extrapolate the results on template and use graphic software or O or write a small program Good luck. V.Kothekar --- Subhash Agarwal wrote: > Hi all > > As James and Boris have written that the solution > they > are able to provide depends on the knowledge of the > user with regards to progam O and understanding of > crystallography. So i would like to say that neither > i > have used program O before nor i am > cryatallographer. > So making things difficult for me. > > While Dr.Nagasuma Chandra writes that i need to be > sure that whether my model has the same quaternary > arrangement as my template or not. Sir in this > regard > i would like to say that the sequence (Query) i have > picked for modelling has known function > (experimentally characterised) and for the same the > template are avaliable and therfore i started > working > on this protein. > > My need to generate the quaternary structure is due > to > reason that i need to observe the active site in the > generated model. Also u state that " it is > relatively > simple to apply the translational and rotational > matrices to obtain a multimer". Can u tell me how > will > u suggest me to do this. > > Moreover if any of u feels that should mail pdb of > generated model and the PDB id of template used, > that > can also be done by me. > > Also i am thankful to everybody as u r trying to > help > me by responding. Please continue to provide > support. > > Thanks > Subhash Agarwal > > ________________________________________________________________________ > Yahoo! India Matrimony: Find your life partner > online > Go to: http://yahoo.shaadi.com/india-matrimony > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________ Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web http://birthday.yahoo.com/netrospective/ From jakechen at iupui.edu Tue Mar 8 00:46:07 2005 From: jakechen at iupui.edu (Chen, Jake) Date: Tue, 8 Mar 2005 00:46:07 -0500 Subject: [BiO BB] CFP: Special Session on Computer Infrastructure for Systems Biology (March 28th Submission Deadline) Message-ID: <9BA28484EAC4B843B4EA7834449D6FFE024BF4D3@iu-mssg-mbx05.exchange.iu.edu> CALL FOR PAPERS 18th International Conference on Systems Engineering (ICSEng'05) Special Session on Computer Infrastructure for Systems Biology August 16-18 2005, Las Vegas, Nevada http://bio.informatics.iupui.edu/bio-05/ ======== Overview ======== The special session's goal is to bring forth ideas and collaborations among industrial and academic bioinformaticians, biocomputing professionals, data analysts, and system biologists to facilitate systems biology research and findings. Both research papers (6 pages, IEEE Proceedings format) and poster papers (2 pages) are solicited to explore case histories of building and maintaining IT infrastructures that support advanced biological research. Both industrial and academic contributions are welcome. ====== Topics ====== Systems Biology is an emerging field that seeks to analyze disparate forms of biological data with an aim of uncovering the function and interaction of the underlying biological systems. It is characterized by voluminous and heterogeneous data, incomplete data sets, low data signal/noise ratios, and extreme difficulties in precisely reproducing experimental conditions. These drawbacks are offset by the profound interest in the field by the Pharmaceutical and Biotechnology industries and by the illumination of biological research in general. We welcome papers/presentations that examine fresh perspectives and profound experiences in the research and development of computer systems enabling systems biology. Topics of interests include (but are not limited to): * Microarray Data Analysis * Functional Imaging and Pattern Recognition * Biological database integration and knowledge representation * Ontologies and semantic web systems for biology * Biomedical literature text mining * Micro-surgery and micro-manipulation * Application of nanotechnology to biological systems * Protein-protein interactions * Proteomics * Protein-small molecule interactions * Metabolic and Genetic Pathways * Visualization of complex data relationships * Biological data tracking and labelling * Clinical Informatics * Laboratory Information Management Systems * Measuring cellular metabolism and cellular signalling ======== AUDIENCE ======== * Computer and IT professionals from the biotechnology and pharmaceutical industries. * Bioinformatics researchers with an interest in real-world applications. * Researchers and developers interested in application of computational systems to biological problems. =============== IMPORTANT DATES =============== Abstracts Due: March 28, 2005 Notification of Acceptance: April 25, 2005 Final paper Due: May 23, 2005 ========== Submission ========== Abstracts in English reporting original and unpublished research results and experience are solicited. All abstracts are to be submitted in PDF or MS word version electronically. Abstracts for refereeing should be double-spaced and must include the special session keyword "Computer Infrastructure for Systems Biology" to reach us correctly. For detailed submission instruction and submission site, go to: http://bio.informatics.iupui.edu/bio-05/submission.stm. Note that submission implies the willingness of at least one of the authors to register and present the paper. All abstracts will be peer reviewed by two indepent members from the scientific committee, and may be accepted into the program as one of the format on a competitive basis: Full papers not to exceed 6 Proceedings-formatted pages, and will be invited for podium presentations; Poster papers not to exceed 2 Proceedings-formatted pages, and will be given a poster board to display work. =========== Publication =========== Accepted and registered papers will be included in the ICSEng'05 conference proceedings published by IEEE Computer Science Press. Selected high-quality full papers will also be published in the International Journal on Computational Intelligence and Applications by World Scientific Publishing Company Press. ================== Contact the Chairs ================== Jake Y. Chen Assistant Professor Indiana University School of Informatics Indianapolis, IN 46202 USA Email: jakechen at iupui.edu Web site: http://bio.informatics.iupui.edu/ Bradley K. Sherman Director of Bioinformatics Mendel Biotechnology, Inc. 21375 Cabot Boulevard Hayward, CA 94545 USA Email: icse at mendelbio.com web site: http://www.mendelbio.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sona_ghn at yahoo.co.in Tue Mar 8 06:17:05 2005 From: sona_ghn at yahoo.co.in (gehana vaswani) Date: Tue, 8 Mar 2005 11:17:05 +0000 (GMT) Subject: [BiO BB] information Message-ID: <20050308111705.58468.qmail@web8502.mail.in.yahoo.com> i am studying B.Tech. bioinformatics in Padmashree d.y. Patil university in India.Does it have enough value &scope here or abroad? Yahoo! India Matrimony: Find your life partneronline. -------------- next part -------------- An HTML attachment was scrubbed... URL: From deletto at unisa.it Tue Mar 8 09:35:57 2005 From: deletto at unisa.it (Davide Eletto) Date: Tue, 08 Mar 2005 15:35:57 +0100 Subject: [BiO BB] Transcription factors prediction In-Reply-To: <20050307175121.64738.qmail@web61301.mail.yahoo.com> References: <20050307175121.64738.qmail@web61301.mail.yahoo.com> Message-ID: <422DB84D.5060907@unisa.it> Hi there, anyone of you could be so kind to give me the name of the most common FREE *Transcription factors prediction *software (online, indeed), that is able to retrieve a list of putative nuclear transc fact. by a DNA sequence? Thanks a lot in advance davide eletto ITALIA (one of six nations) From virajj at lycos.com Tue Mar 8 09:42:06 2005 From: virajj at lycos.com (vijaya raj) Date: Tue, 08 Mar 2005 09:42:06 -0500 Subject: [BiO BB] information Message-ID: <20050308144206.1D214C6132@ws7-5.us4.outblaze.com> An HTML attachment was scrubbed... URL: From hz5 at njit.edu Tue Mar 8 10:00:17 2005 From: hz5 at njit.edu (hz5 at njit.edu) Date: Tue, 08 Mar 2005 10:00:17 -0500 (EST) Subject: [BiO BB] Transcription factors prediction In-Reply-To: <422DB84D.5060907@unisa.it> References: <20050307175121.64738.qmail@web61301.mail.yahoo.com> <422DB84D.5060907@unisa.it> Message-ID: <1110294017.422dbe01e0a74@webmail.njit.edu> TRANSFAC (http://www.gene-regulation.com/) TFSearch (http://mbs.cbrc.jp/research/db/TFSEARCH.html) TESS (http://www.cbil.upenn.edu/cgi-bin/tess/tess33?RQ=WELCOME) TRANSFAC is the most comprehensive, TFSearch is using old TRANSFAC matrix. They are all online, transfac may need to pay if any downstream product or non- research related stuff involved (not sure). Quoting Davide Eletto : > > > Hi there, > anyone of you could be so kind to give me the name of the most common > FREE *Transcription factors prediction *software (online, indeed), that > > is able to retrieve a list of putative nuclear transc fact. by a DNA > sequence? > > Thanks a lot in advance > > davide eletto > ITALIA (one of six nations) > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ========================================================= Haibo Zhang, PhD student Computational Biology, NJIT & Rutgers University Center for Applied Genomics, PHRI http://afs13.njit.edu/~hz5 From logan at cacs.louisiana.edu Tue Mar 8 15:44:14 2005 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Tue, 8 Mar 2005 14:44:14 -0600 Subject: [BiO BB] information In-Reply-To: <20050308111705.58468.qmail@web8502.mail.in.yahoo.com> Message-ID: <002001c5241f$9a109010$454d4682@win.cacs.louisiana.edu> Knowing and watching the best people in any field suggest me that one should pursue a field or a discipline because he/she likes the field not because there are opportunity out there. Bioinformatics is not for faint heart!! Many of the problems are NP-hard and one need a lot of innovation, perseverance and dedication to contribute in this field. If you do not like it, do not push it because there are jobs out there. Follow your heart.. Good luck Raja Loganantharaj -----Original Message----- From: bio_bulletin_board-bounces+logan=cacs.louisiana.edu at bioinformatics.org [mailto:bio_bulletin_board-bounces+logan=cacs.louisiana.edu at bioinformati cs.org] On Behalf Of gehana vaswani Sent: Tuesday, March 08, 2005 5:17 AM To: BiO_Bulletin_Board at bioinformatics.org Subject: [BiO BB] information i am studying B.Tech. bioinformatics in Padmashree d.y. Patil university in India.Does it have enough value &scope here or abroad? Yahoo! India Matrimony: Find your life partner online . -------------- next part -------------- An HTML attachment was scrubbed... URL: From atariml at email.it Tue Mar 8 16:50:40 2005 From: atariml at email.it (Andrea Franceschini) Date: Tue, 8 Mar 2005 22:50:40 +0100 Subject: [BiO BB] Transcription factors prediction References: <20050307175121.64738.qmail@web61301.mail.yahoo.com> <422DB84D.5060907@unisa.it> Message-ID: <005301c52428$e0cf4920$0401a8c0@atarippc> In "Nature Biotechnology 23, 137 - 144 Published online: 06 January 2005; Assessing computational tools for the discovery of transcription factor binding sites" you can find the unswer to your question. http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v23/n1/full/nbt1053.html The suggestion in the article to obtain the best results is to analyze your sequences with both these software : Weeder Web: http://159.149.109.16:8080/weederWeb/ Motif Sampler: http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html Andrea Franceschini ----- Original Message ----- From: "Davide Eletto" To: "The general forum at Bioinformatics.Org" Sent: Tuesday, March 08, 2005 3:35 PM Subject: [BiO BB] Transcription factors prediction > Hi there, > anyone of you could be so kind to give me the name of the most common FREE > *Transcription factors prediction *software (online, indeed), that is able > to retrieve a list of putative nuclear transc fact. by a DNA sequence? > > Thanks a lot in advance > > davide eletto > ITALIA (one of six nations) > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jstroud at mbi.ucla.edu Tue Mar 8 17:23:16 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Tue, 8 Mar 2005 14:23:16 -0800 Subject: [BiO BB] Transcription factors prediction In-Reply-To: <005301c52428$e0cf4920$0401a8c0@atarippc> References: <20050307175121.64738.qmail@web61301.mail.yahoo.com> <422DB84D.5060907@unisa.it> <005301c52428$e0cf4920$0401a8c0@atarippc> Message-ID: <200503081423.16965.jstroud@mbi.ucla.edu> Not that it answers your question, but here is a critical read on the subject: Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. Nature. 2005 Feb 27; [Epub ahead of print] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15735639 James On Tuesday 08 March 2005 01:50 pm, Andrea Franceschini wrote: > In "Nature Biotechnology 23, 137 - 144 Published online: 06 January > 2005; Assessing computational tools for the discovery of transcription > factor binding sites" you can find the unswer to your question. > http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v23/n1/full/nb >t1053.html > > The suggestion in the article to obtain the best results is to analyze your > sequences with both these software : > Weeder Web: http://159.149.109.16:8080/weederWeb/ > Motif Sampler: http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html > > > > Andrea Franceschini > > > > > > ----- Original Message ----- > From: "Davide Eletto" > To: "The general forum at Bioinformatics.Org" > > Sent: Tuesday, March 08, 2005 3:35 PM > Subject: [BiO BB] Transcription factors prediction > > > Hi there, > > anyone of you could be so kind to give me the name of the most common > > FREE *Transcription factors prediction *software (online, indeed), that > > is able to retrieve a list of putative nuclear transc fact. by a DNA > > sequence? > > > > Thanks a lot in advance > > > > davide eletto > > ITALIA (one of six nations) > > _______________________________________________ > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- James Stroud, Ph.D. UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 From mkgovindis at yahoo.com Tue Mar 8 23:48:47 2005 From: mkgovindis at yahoo.com (govind mk) Date: Tue, 8 Mar 2005 20:48:47 -0800 (PST) Subject: [BiO BB] Transcription factors prediction In-Reply-To: 6667 Message-ID: <20050309044847.76339.qmail@web54505.mail.yahoo.com> Hi all Continuing on the same discussion of transcription factors ? I would like to know if there is any database which can give me a list of binding sites for a given transcription factor. Refards, M.K.Govind --- James Stroud wrote: > Not that it answers your question, but here is a > critical read on the subject: > > Systematic discovery of regulatory motifs in human > promoters and 3' UTRs by > comparison of several mammals. > Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, > Lindblad-Toh K, Lander ES, > Kellis M. > Nature. 2005 Feb 27; [Epub ahead of print] > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15735639 > > James > > On Tuesday 08 March 2005 01:50 pm, Andrea > Franceschini wrote: > > In "Nature Biotechnology 23, 137 - 144 > Published online: 06 January > > 2005; Assessing computational tools for the > discovery of transcription > > factor binding sites" you can find the unswer to > your question. > > > http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v23/n1/full/nb > >t1053.html > > > > The suggestion in the article to obtain the best > results is to analyze your > > sequences with both these software : > > Weeder Web: http://159.149.109.16:8080/weederWeb/ > > Motif Sampler: > http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html > > > > > > > > Andrea Franceschini > > > > > > > > > > > > ----- Original Message ----- > > From: "Davide Eletto" > > To: "The general forum at Bioinformatics.Org" > > > > Sent: Tuesday, March 08, 2005 3:35 PM > > Subject: [BiO BB] Transcription factors prediction > > > > > Hi there, > > > anyone of you could be so kind to give me the > name of the most common > > > FREE *Transcription factors prediction *software > (online, indeed), that > > > is able to retrieve a list of putative nuclear > transc fact. by a DNA > > > sequence? > > > > > > Thanks a lot in advance > > > > > > davide eletto > > > ITALIA (one of six nations) > > > _______________________________________________ > > > Bioinformatics.Org general forum - > > > BiO_Bulletin_Board at bioinformatics.org > > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- > James Stroud, Ph.D. > UCLA-DOE Institute for Genomics and Proteomics > Box 951570 > Los Angeles, CA 90095 > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________ Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web http://birthday.yahoo.com/netrospective/ From frcerqueira at gmail.com Wed Mar 9 13:49:42 2005 From: frcerqueira at gmail.com (Fabio Cerqueira) Date: Wed, 9 Mar 2005 15:49:42 -0300 Subject: [BiO BB] data for clustering test Message-ID: <50fceb2c0503091049a0f74dc@mail.gmail.com> Hi all, I want to test a new approach for clustering on microarray data and my focus is exclusively make cluster. I have no interest in raw data or how to calculate the distance matrix, but in how I make clustering on it. So, the ideal situation would be get distance matrices and some good previous results (with some good algorithm) of clustering on them. A distance matrix will be the entry to my program. After the execution, I would compare my results with the previous one, so I 'll be able to compare if my clustering method is as good as others. Does anyone know a source containing distance matrices and previous results of clustering on them? Once again, the raw data is not my interest, since my focus is not distance calculation, but clustering. Thanks, . F?bio . From logan at cacs.louisiana.edu Wed Mar 9 17:09:49 2005 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Wed, 9 Mar 2005 16:09:49 -0600 Subject: [BiO BB] Second Call for paper/participation of 2nd Annual Bioinformatics Symposium April 18, 2005 In-Reply-To: <50fceb2c0503091049a0f74dc@mail.gmail.com> Message-ID: <002801c524f4$bc012920$454d4682@win.cacs.louisiana.edu> Place: Lafayette, Louisiana Date: April 18, 2005 Paper due: March 20, 2005 Symposium web site: http://www.cacs.louisiana.edu/bioinformatics/symp05/index.html You are invited to submit a paper to the Second Annual Bioinformatics Symposium 2005. The symposium's goal is to build a bridge among the researchers working in industries, academic and research institutions. This forum will provide an opportunity to learn and to understand the ongoing research activities that may help spark some new collaboration for future research and funding opportunities in this area. Those who are working in the area of molecular biology, computer science, and statistics are encouraged to participate in the symposium to acquaint with the current research agenda of Bioinformatics and to be informed about potential funding sources. Accepted papers will be scheduled for a short podium presentations, and will be published in the conference proceedings. Please submit a complete paper or an extended abstract up to 5 pages. Computer science papers must show biological relevance, and biology papers must stress the computational contribution to the results. The keynote speakers will include: Professor Philip E. Bourne Professor of Pharmacology, UCSD Co-Director Protein Data Bank, SDSC Editor-in-Chief PLoS Computational Biology Dr. Fern Y. Hunt Mathematical and Computational Sciences Division National Institute of Standards and Technology (NIST) Dr. Mark Gosink Head of Computational Biology, Scripps Florida Participation: Registration is required to attend the symposium. On line registration is opened while seats are available. Thank you for your time Raja Loganantharaj Bioinformatics Symposium Organizers From forward at hongyu.org Wed Mar 9 20:39:54 2005 From: forward at hongyu.org (Hongyu Zhang) Date: Wed, 9 Mar 2005 17:39:54 -0800 Subject: [BiO BB] PSI-BLAST query filter Message-ID: <1110418794.422fa56a5437d@hongyu.org> Dear all, I have a group of low complexity sequences here, based on them I want to create a PSI-BLAST alignment. The problem is that when running PSI-BLAST, it will automatically filter out the low complexity region in the query sequence, which then will cause the query to have no hit to the rest subject sequences. In BLASTP, I can just use the "-F f" option to turn off the filter, but the PSI-BLAST (blastpgp) doesn't seem to be affected by this option. NCBI help desk provides little help unfortunately. Please let me know if any of you have solutions. Thanks in advance. -- Hongyu Zhang Computational biologist Ceres Inc. From idoerg at burnham.org Wed Mar 9 21:15:13 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 09 Mar 2005 18:15:13 -0800 Subject: [BiO BB] PSI-BLAST query filter In-Reply-To: <1110418794.422fa56a5437d@hongyu.org> References: <1110418794.422fa56a5437d@hongyu.org> Message-ID: <422FADB1.5070108@burnham.org> blastpgp "-F F" turns the filtering off, which is what you want (and which is the default, incidentally). I just checked blastpgp 2.2.5 and it does not filter low complexity sequences. In blastall, the default is "-F T"; this is done to confuse us and keep us on our toes. The broader picture: why would you want to use low complexity sequences in PSI-BLAST? They'll bring you all sorts of non-specific stuff, which will also be unrelated to the pattern you think you are searching for. There are programs to search for low complexity regions. 0j.py comes to mind, but there are others. best, Iddo Hongyu Zhang wrote: >Dear all, > >I have a group of low complexity sequences here, based on them I want >to create a PSI-BLAST alignment. The problem is that when running >PSI-BLAST, it will automatically filter out the low complexity region >in the query sequence, which then will cause the query to have no hit >to the rest subject sequences. In BLASTP, I can just use the "-F f" >option to turn off the filter, but the PSI-BLAST (blastpgp) doesn't >seem to be affected by this option. > >NCBI help desk provides little help unfortunately. Please let me know >if any of you have solutions. Thanks in advance. > > >-- >Hongyu Zhang >Computational biologist >Ceres Inc. > > > > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo ========================== The First Automated Protein Function Prediction SIG Detroit, MI June 24, 2005 http://ffas.burnham.org/AFP From forward at hongyu.org Thu Mar 10 00:51:59 2005 From: forward at hongyu.org (Hongyu Zhang) Date: Wed, 9 Mar 2005 21:51:59 -0800 Subject: [BiO BB] PSI-BLAST query filter In-Reply-To: <422FADB1.5070108@burnham.org> References: <1110418794.422fa56a5437d@hongyu.org> <422FADB1.5070108@burnham.org> Message-ID: <1110433919.422fe07f8da09@hongyu.org> Thanks. Actually I did try the "-F F" option in blastpgp, but it doesn't work. I am not using PSI-BLAST to do any search. I am just trying to generate an alignment give a group of low complexity sequences. I could use ClustalW, but my downstream program requires PSI-BLAST alignment format. -- Hongyu Zhang Computational biologist Ceres Inc. Quoting Iddo Friedberg : > blastpgp "-F F" turns the filtering off, which is what you want > (and > which is the default, incidentally). I just checked blastpgp 2.2.5 > and > it does not filter low complexity sequences. In blastall, the > default is > "-F T"; this is done to confuse us and keep us on our toes. > > The broader picture: why would you want to use low complexity > sequences > in PSI-BLAST? They'll bring you all sorts of non-specific stuff, > which > will also be unrelated to the pattern you think you are searching > for. > There are programs to search for low complexity regions. 0j.py > comes to > mind, but there are others. > > best, > > Iddo > > Hongyu Zhang wrote: > > >Dear all, > > > >I have a group of low complexity sequences here, based on them I > want > >to create a PSI-BLAST alignment. The problem is that when running > >PSI-BLAST, it will automatically filter out the low complexity > region > >in the query sequence, which then will cause the query to have no > hit > >to the rest subject sequences. In BLASTP, I can just use the "-F > f" > >option to turn off the filter, but the PSI-BLAST (blastpgp) > doesn't > >seem to be affected by this option. > > > >NCBI help desk provides little help unfortunately. Please let me > know > >if any of you have solutions. Thanks in advance. > > > > > >-- > >Hongyu Zhang > >Computational biologist > >Ceres Inc. > > > > > > > > > > > >_______________________________________________ > >Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 USA > Tel: +1 (858) 646 3100 x3516 > http://ffas.ljcrf.edu/~iddo > ========================== > The First Automated Protein Function Prediction SIG > Detroit, MI June 24, 2005 > http://ffas.burnham.org/AFP > > From idoerg at burnham.org Thu Mar 10 01:12:03 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 9 Mar 2005 22:12:03 -0800 Subject: [BiO BB] PSI-BLAST query filter In-Reply-To: <1110433919.422fe07f8da09@hongyu.org> Message-ID: OK, I still do not understand why blastpgp insists on filtering your sequence... which version are you using? Not that: 1) Using blastpgp You won't get a multiple alignment. You will get a multiple pairwise alignment to the query sequence. Using ClustalW you will get a true multiple alignment. 2) There is still an inherent problem when aligning low complexity sequences. 3) If those two factors do not matter, then why not use blastall to build your alignment? Why do oyu need the iterations blastpgp offers? Curious, ./I On Wed, 9 Mar 2005, Hongyu Zhang wrote: > Thanks. Actually I did try the "-F F" option in blastpgp, but it > doesn't work. > > I am not using PSI-BLAST to do any search. I am just trying to > generate an alignment give a group of low complexity sequences. I > could use ClustalW, but my downstream program requires PSI-BLAST > alignment format. > > -- > Hongyu Zhang > Computational biologist > Ceres Inc. > > > > Quoting Iddo Friedberg : > > > blastpgp "-F F" turns the filtering off, which is what you want > > (and > > which is the default, incidentally). I just checked blastpgp 2.2.5 > > and > > it does not filter low complexity sequences. In blastall, the > > default is > > "-F T"; this is done to confuse us and keep us on our toes. > > > > The broader picture: why would you want to use low complexity > > sequences > > in PSI-BLAST? They'll bring you all sorts of non-specific stuff, > > which > > will also be unrelated to the pattern you think you are searching > > for. > > There are programs to search for low complexity regions. 0j.py > > comes to > > mind, but there are others. > > > > best, > > > > Iddo > > > > Hongyu Zhang wrote: > > > > >Dear all, > > > > > >I have a group of low complexity sequences here, based on them I > > want > > >to create a PSI-BLAST alignment. The problem is that when running > > >PSI-BLAST, it will automatically filter out the low complexity > > region > > >in the query sequence, which then will cause the query to have no > > hit > > >to the rest subject sequences. In BLASTP, I can just use the "-F > > f" > > >option to turn off the filter, but the PSI-BLAST (blastpgp) > > doesn't > > >seem to be affected by this option. > > > > > >NCBI help desk provides little help unfortunately. Please let me > > know > > >if any of you have solutions. Thanks in advance. > > > > > > > > >-- > > >Hongyu Zhang > > >Computational biologist > > >Ceres Inc. > > > > > > > > > > > > > > > > > >_______________________________________________ > > >Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > > > > > > > > -- > > Iddo Friedberg, Ph.D. > > The Burnham Institute > > 10901 N. Torrey Pines Rd. > > La Jolla, CA 92037 USA > > Tel: +1 (858) 646 3100 x3516 > > http://ffas.ljcrf.edu/~iddo > > ========================== > > The First Automated Protein Function Prediction SIG > > Detroit, MI June 24, 2005 > > http://ffas.burnham.org/AFP > > > > > From forward at hongyu.org Thu Mar 10 01:29:33 2005 From: forward at hongyu.org (Hongyu Zhang) Date: Wed, 9 Mar 2005 22:29:33 -0800 Subject: [BiO BB] PSI-BLAST query filter In-Reply-To: References: Message-ID: <1110436173.422fe94d6b6e4@hongyu.org> Iddo, What I meant is using "-m 1" option in blastpgp to create an alignment view of multiple sequences. The version of my blast program is 2.2.8 running on Linux. I prefer blastpgp because it allows me the flexibility to do multiple iterations to increase the alignment accuracy. You are right that, in the end, I might have to use blastall to generate alignment if blastpgp keeps giving me trouble. Thanks! -- Hongyu Zhang Computational biologist Ceres Inc. Quoting Iddo Friedberg : > > OK, I still do not understand why blastpgp insists on filtering > your > sequence... which version are you using? > > Not that: > > 1) Using blastpgp You won't get a multiple alignment. You will get > a > multiple pairwise alignment to the query sequence. Using ClustalW > you will > get a true multiple alignment. > > 2) There is still an inherent problem when aligning low complexity > sequences. > > 3) If those two factors do not matter, then why not use blastall to > build > your alignment? Why do oyu need the iterations blastpgp offers? > > Curious, > > ./I > > > > On Wed, 9 Mar 2005, Hongyu Zhang wrote: > > > Thanks. Actually I did try the "-F F" option in blastpgp, but it > > doesn't work. > > > > I am not using PSI-BLAST to do any search. I am just trying to > > generate an alignment give a group of low complexity sequences. I > > could use ClustalW, but my downstream program requires PSI-BLAST > > alignment format. > > > > -- > > Hongyu Zhang > > Computational biologist > > Ceres Inc. > > > > > > > > Quoting Iddo Friedberg : > > > > > blastpgp "-F F" turns the filtering off, which is what you want > > > (and > > > which is the default, incidentally). I just checked blastpgp > 2.2.5 > > > and > > > it does not filter low complexity sequences. In blastall, the > > > default is > > > "-F T"; this is done to confuse us and keep us on our toes. > > > > > > The broader picture: why would you want to use low complexity > > > sequences > > > in PSI-BLAST? They'll bring you all sorts of non-specific > stuff, > > > which > > > will also be unrelated to the pattern you think you are > searching > > > for. > > > There are programs to search for low complexity regions. 0j.py > > > comes to > > > mind, but there are others. > > > > > > best, > > > > > > Iddo > > > > > > Hongyu Zhang wrote: > > > > > > >Dear all, > > > > > > > >I have a group of low complexity sequences here, based on them > I > > > want > > > >to create a PSI-BLAST alignment. The problem is that when > running > > > >PSI-BLAST, it will automatically filter out the low complexity > > > region > > > >in the query sequence, which then will cause the query to have > no > > > hit > > > >to the rest subject sequences. In BLASTP, I can just use the > "-F > > > f" > > > >option to turn off the filter, but the PSI-BLAST (blastpgp) > > > doesn't > > > >seem to be affected by this option. > > > > > > > >NCBI help desk provides little help unfortunately. Please let > me > > > know > > > >if any of you have solutions. Thanks in advance. > > > > > > > > > > > >-- > > > >Hongyu Zhang > > > >Computational biologist > > > >Ceres Inc. > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > >Bioinformatics.Org general forum - > > > BiO_Bulletin_Board at bioinformatics.org > > > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > Iddo Friedberg, Ph.D. > > > The Burnham Institute > > > 10901 N. Torrey Pines Rd. > > > La Jolla, CA 92037 USA > > > Tel: +1 (858) 646 3100 x3516 > > > http://ffas.ljcrf.edu/~iddo > > > ========================== > > > The First Automated Protein Function Prediction SIG > > > Detroit, MI June 24, 2005 > > > http://ffas.burnham.org/AFP > > > > > > > > > > From kevin_berney at yahoo.com Thu Mar 10 12:05:27 2005 From: kevin_berney at yahoo.com (Kevin Berney) Date: Thu, 10 Mar 2005 09:05:27 -0800 (PST) Subject: [BiO BB] Re: PSI-BLAST query filter In-Reply-To: <20050310063835.249B6D1F86@www.bioinformatics.org> Message-ID: <20050310170527.22697.qmail@web50206.mail.yahoo.com> a clarification perhaps, but doesn't psi-blast give a list of pairwise alignments to a -- "consensus" sequence. or maybe a weight matrix? whereas blast would just give you a list of pairwise alignments to the original query sequence. these ought to produce very different results. though neither is a true multiple alignment. Kevin Berney Quoting Iddo ============ OK, I still do not understand why blastpgp insists on filtering your sequence... which version are you using? Not that: 1) Using blastpgp You won't get a multiple alignment. You will get a multiple pairwise alignment to the query sequence. Using ClustalW you will get a true multiple alignment. 2) There is still an inherent problem when aligning low complexity sequences. 3) If those two factors do not matter, then why not use blastall to build your alignment? Why do oyu need the iterations blastpgp offers? Curious, ./I __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From idoerg at burnham.org Thu Mar 10 12:37:24 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 10 Mar 2005 09:37:24 -0800 Subject: [BiO BB] Re: PSI-BLAST query filter In-Reply-To: <20050310170527.22697.qmail@web50206.mail.yahoo.com> References: <20050310170527.22697.qmail@web50206.mail.yahoo.com> Message-ID: <423085D4.5080605@burnham.org> Kevin, The first round of PSI-BLAST is actually a regular BLASTP, but which generates a position specific score matrix. (NOT a consensus sequence). The second round is an alignment to the PSSM, generateing a new PSSM, and so on, ad nauseum or convergence (i.e. no new sequences). You are right, neither is a true multiple alignment. ./I Kevin Berney wrote: >a clarification perhaps, but doesn't psi-blast give a >list of pairwise alignments to a -- "consensus" >sequence. or maybe a weight matrix? > >whereas blast would just give you a list of pairwise >alignments to the original query sequence. > >these ought to produce very different results. though >neither is a true multiple alignment. > >Kevin Berney > > > >Quoting Iddo >============ >OK, I still do not understand why blastpgp insists on >filtering your >sequence... which version are you using? > >Not that: > >1) Using blastpgp You won't get a multiple alignment. >You will get a >multiple pairwise alignment to the query sequence. >Using ClustalW you will >get a true multiple alignment. > >2) There is still an inherent problem when aligning >low complexity >sequences. > >3) If those two factors do not matter, then why not >use blastall to build >your alignment? Why do oyu need the iterations >blastpgp offers? > >Curious, > >./I > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo ========================== The First Automated Protein Function Prediction SIG Detroit, MI June 24, 2005 http://ffas.burnham.org/AFP From forward at hongyu.org Fri Mar 11 14:24:11 2005 From: forward at hongyu.org (Hongyu Zhang) Date: Fri, 11 Mar 2005 11:24:11 -0800 Subject: [BiO BB] Re: PSI-BLAST query filter (Kevin Berney) Message-ID: <1110569051.4231f05bb1661@hongyu.org> It's true that PSI-BLAST perhaps was not designed to be used as a general purpose multiple alignment program as ClustalW was, but according to my observation lots of time its result is better than ClustalW. The problem of ClustalW is that, for a group of remote, and sometimes not so remote, homologous sequences, it often gives funny alignments. The situation can be worsened if the group has lots of sequences; meanwhile, PSI-BLAST alignment is much better in handling those situations. Again, for those who are not familiar with NCBI-BLAST, it provides the "-m 1" option to print out the multiple squence alignment instead of the default pair-wise alignment. I assume most standard multiple sequence alignment methods are just multi-steps of pair-wise alignments in an optimized order, while profile methods are smarter in looking for some common patterns in an iterated fashion. I used a GUI version of ClustalW-based program a long long time ago (I forgot the program name), which also provides a profile option in its menu, but I didn't remember how well it works. Actually, some benchmarks on this topic would be nice. -- Hongyu Zhang Computational biologist Ceres Inc. From idoerg at burnham.org Fri Mar 11 14:47:36 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 11 Mar 2005 11:47:36 -0800 Subject: [BiO BB] Re: PSI-BLAST query filter (Kevin Berney) In-Reply-To: <1110569051.4231f05bb1661@hongyu.org> References: <1110569051.4231f05bb1661@hongyu.org> Message-ID: <4231F5D8.1000109@burnham.org> Hongyu Zhang wrote: >It's true that PSI-BLAST perhaps was not designed to be used as a >general purpose multiple alignment program as ClustalW was, but >according to my observation lots of time its result is better than >ClustalW. The problem of ClustalW is that, for a group of remote, and >sometimes not so remote, homologous sequences, it often gives >funny alignments. The situation can be worsened if the group has lots >of sequences; meanwhile, PSI-BLAST alignment is much better in >handling those situations. Again, for those who are not familiar with >NCBI-BLAST, it provides the "-m 1" option to print out the multiple >squence alignment instead of the default pair-wise alignment. > > The -m flag is cosmetic. The alignments you see are still pairwise alignments to the query sequence, not a multiple alignment. -m 1 gives you the full sequences, as opposed to only the HSPs. (Note that HSPs may overlap, which can give you some interesting results when you use "-m 1"). The reason PSI-BLAST "beavior" seems "better" is that it is performing pairwise alignments to a single sequence, so naturally the alignments would seem more ordered. ClustalW would give you "funny alignemnts" as beyond some point it is not equipped to handle long and/or low complexity and/or large numbers and/or distantly related sequences. T-COFFEE gives you more mileage in that respect, you might want to try that if you need a true MSA. It all boils down to your biological question: whether it requires a true multiple alignment, for which the BLAST programs are not suited, or it just requires a bunch of sequences to "toe the line" of the original query. >I assume most standard multiple sequence alignment methods are just >multi-steps of pair-wise alignments in an optimized order, while >profile methods are smarter in looking for some common >patterns in an iterated fashion. I used a GUI version of >ClustalW-based program a long long time ago (I forgot the >program name), which also provides a profile option in its menu, but I >didn't remember how well it works. Actually, some benchmarks on this >topic would be nice. > >-- >Hongyu Zhang >Computational biologist >Ceres Inc. > > > > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo ========================== The First Automated Protein Function Prediction SIG Detroit, MI June 24, 2005 http://ffas.burnham.org/AFP From vetdebarshi at gmail.com Fri Mar 11 15:22:47 2005 From: vetdebarshi at gmail.com (debarshi roy) Date: Fri, 11 Mar 2005 14:22:47 -0600 Subject: [BiO BB] Re: PSI-BLAST query filter (Kevin Berney) In-Reply-To: <1110569051.4231f05bb1661@hongyu.org> References: <1110569051.4231f05bb1661@hongyu.org> Message-ID: <95907580503111222613adcf4@mail.gmail.com> Hi Mr.Zhang, I am a Graduate student in Biology major in Wichita State University. I am interested to join in the Bioinformatics Lab in my University and start my research works on gene expression and some other on going projects of K-BRIN program. Could you please help me by providing with some basic informations? I would like to know aboput the prerequisite knowledge for Bioinformatics research What are computer programming language which are of most importance? and what are the lab techniques needed ? Earlier I have done Bachelors of Veterinary sc and animal Husbandry from India. Please give me the informations I will be very much greatful to you. Thanks. Dr.Debarshi Roy On Fri, 11 Mar 2005 11:24:11 -0800, Hongyu Zhang wrote: > It's true that PSI-BLAST perhaps was not designed to be used as a > general purpose multiple alignment program as ClustalW was, but > according to my observation lots of time its result is better than > ClustalW. The problem of ClustalW is that, for a group of remote, and > sometimes not so remote, homologous sequences, it often gives > funny alignments. The situation can be worsened if the group has lots > of sequences; meanwhile, PSI-BLAST alignment is much better in > handling those situations. Again, for those who are not familiar with > NCBI-BLAST, it provides the "-m 1" option to print out the multiple > squence alignment instead of the default pair-wise alignment. > > I assume most standard multiple sequence alignment methods are just > multi-steps of pair-wise alignments in an optimized order, while > profile methods are smarter in looking for some common > patterns in an iterated fashion. I used a GUI version of > ClustalW-based program a long long time ago (I forgot the > program name), which also provides a profile option in its menu, but I > didn't remember how well it works. Actually, some benchmarks on this > topic would be nice. > > -- > Hongyu Zhang > Computational biologist > Ceres Inc. > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From jeff at bioinformatics.org Wed Mar 16 10:39:49 2005 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 16 Mar 2005 10:39:49 -0500 Subject: [BiO BB] CfP: BiOAM 2005 Open-Access Conference Message-ID: <42385345.5050501@bioinformatics.org> GENERAL CALL FOR PARTICIPATION 2005 ANNUAL MEETING OF THE BIOINFORMATICS ORGANIZATION MAY 17-19, 2005 HYNES AUDITORIUM, BOSTON IMPORTANT DATES: Deadline for submitting abstracts: Friday, April 1, 2005 (extended) Notification of acceptance: Monday, April 4, 2005 (extended) Annual meeting special track: Thursday, May 19, 2005, 1 PM to 4 PM The Bioinformatics Organization (Bioinformatics.Org) invites you to present your open-access project, hosted at Bioinformatics.Org or elsewhere, at the 5th Annual Meeting (BiOAM 2005), to be held in conjunction with the Bio-IT World Conference & Expo. We are seeking 45-minute slide-show presentations to be given to an audience of 50 to 100 people, open to all attendees of Bio-IT World, Boston. Format and subject matter should be similar to those of past presentations, which have generally been broad in scope: 2003: http://conferences.oreillynet.com/pub/w/21/bio_org.html 2002: http://conferences.oreillynet.com/cs/bio2002/pub/w/17/bio_org.html 2001: http://bioinformatics.org/events/2001/brie-oap/ (The 2004 Meeting involved participation in the Bioclusters Workshop: http://bioclusters.org/) If you or any of the members of your project are interested in presenting, please send me an abstract by April 1st (no fooling): jeff at bioinformatics.org Presenters will have free access to portions of the Bio-IT World Conference & Expo. Cheers. Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From pjain at xldb.di.fc.ul.pt Thu Mar 10 02:51:52 2005 From: pjain at xldb.di.fc.ul.pt (Pooja Jain) Date: Thu, 10 Mar 2005 07:51:52 +0000 Subject: [BiO BB] Transcription factors prediction In-Reply-To: <20050309044847.76339.qmail@web54505.mail.yahoo.com> References: <20050309044847.76339.qmail@web54505.mail.yahoo.com> Message-ID: <1110441112.422ffc98196c1@webservices.di.fc.ul.pt> Hi Govind, Please have a look at YeaSTRACT, (www.yeastract.com). It can give you the documented binding sites for a given yeast TFs. Best Regards, -Pooja Quoting govind mk : > Hi all > > Continuing on the same discussion of transcription > factors ? I would like to know if there is any > database which can give me a list of binding sites for > a given transcription factor. > > Refards, > M.K.Govind > > > --- James Stroud wrote: > > Not that it answers your question, but here is a > > critical read on the subject: > > > > Systematic discovery of regulatory motifs in human > > promoters and 3' UTRs by > > comparison of several mammals. > > Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, > > Lindblad-Toh K, Lander ES, > > Kellis M. > > Nature. 2005 Feb 27; [Epub ahead of print] > > > > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15735639 > > > > James > > > > On Tuesday 08 March 2005 01:50 pm, Andrea > > Franceschini wrote: > > > In "Nature Biotechnology 23, 137 - 144 > > Published online: 06 January > > > 2005; Assessing computational tools for the > > discovery of transcription > > > factor binding sites" you can find the unswer to > > your question. > > > > > > http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v23/n1/full/nb > > >t1053.html > > > > > > The suggestion in the article to obtain the best > > results is to analyze your > > > sequences with both these software : > > > Weeder Web: http://159.149.109.16:8080/weederWeb/ > > > Motif Sampler: > > > http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html > > > > > > > > > > > > Andrea Franceschini > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: "Davide Eletto" > > > To: "The general forum at Bioinformatics.Org" > > > > > > Sent: Tuesday, March 08, 2005 3:35 PM > > > Subject: [BiO BB] Transcription factors prediction > > > > > > > Hi there, > > > > anyone of you could be so kind to give me the > > name of the most common > > > > FREE *Transcription factors prediction *software > > (online, indeed), that > > > > is able to retrieve a list of putative nuclear > > transc fact. by a DNA > > > > sequence? > > > > > > > > Thanks a lot in advance > > > > > > > > davide eletto > > > > ITALIA (one of six nations) > > > > _______________________________________________ > > > > Bioinformatics.Org general forum - > > > > BiO_Bulletin_Board at bioinformatics.org > > > > > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > _______________________________________________ > > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > > > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- > > James Stroud, Ph.D. > > UCLA-DOE Institute for Genomics and Proteomics > > Box 951570 > > Los Angeles, CA 90095 > > _______________________________________________ > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > __________________________________ > Celebrate Yahoo!'s 10th Birthday! > Yahoo! Netrospective: 100 Moments of the Web > http://birthday.yahoo.com/netrospective/ > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From seematrivedi at sify.com Mon Mar 14 13:46:44 2005 From: seematrivedi at sify.com (Seema Trivedi) Date: Tue, 15 Mar 2005 00:16:44 +0530 Subject: [BiO BB] random sequences Message-ID: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> Dr. Boris Steipe, I will be highly obliged if you could kindly let me know if there are any softwares which I can use for generation of random sequences of nucleotides. I need to do this with large sequences. Thank you Sorry for the trouble, seema -------------- next part -------------- An HTML attachment was scrubbed... URL: From forward at hongyu.org Tue Mar 15 23:05:19 2005 From: forward at hongyu.org (Hongyu Zhang) Date: Tue, 15 Mar 2005 20:05:19 -0800 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 5, Issue 13 In-Reply-To: <20050312170304.CB993D1F69@www.bioinformatics.org> References: <20050312170304.CB993D1F69@www.bioinformatics.org> Message-ID: <1110945919.4237b07f70018@hongyu.org> > The -m flag is cosmetic. The alignments you see are still pairwise > alignments to the query sequence, not a multiple alignment. -m 1 Iddo, I agree to most of your points, however, since PSI-BLAST uses the PSSM (Position Specific Score Matrix), I would argue that the final alignment contains more than just a pair-wise alignment. PSSM is built upon the multiple sequences aligned in the previous round of iterations. > Could you please help me by providing with some basic informations? > I would like to know aboput the prerequisite knowledge for > Bioinformatics research What are computer programming language > which > are of most importance? > and what are the lab techniques needed ? Hi Deharshi. C/C++, Java and Perl are most important languages in bioinformatics. C/C++ is more popular on speed sensitive applications, while Java and Perl are more popular on database and web related applications. C# is also catching up recently. In addition to computer languages, you should take some classes on algorithm development and statistics, which will make you more than just a bioinformatics programmer. From jstroud at mbi.ucla.edu Wed Mar 16 20:05:49 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Wed, 16 Mar 2005 17:05:49 -0800 Subject: [BiO BB] random sequences In-Reply-To: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> References: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> Message-ID: <200503161705.49792.jstroud@mbi.ucla.edu> Python can do this with about 5 lines if you don't have a polynomial distribution and about 8 if you do. Download and install python and run this program (you will need to consult the manual to figure out how to run python programs--pretty easy though). Work through the "hello world" example to get started, then run the following program. from random import choice seq_len = 100 choices = ("A","T","G","C") the_seq = "" for abase in xrange(seq_len): the_seq += choice(choices) print the_seq If you have polynomial distributions, its a little more complicated James On Monday 14 March 2005 10:46 am, Seema Trivedi wrote: > Dr. Boris Steipe, > I will be highly obliged if you could kindly let me know if there are any > softwares which I can use for generation of random sequences of > nucleotides. I need to do this with large sequences. Thank you > Sorry for the trouble, > seema -- James Stroud, Ph.D. UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 From landman at scalableinformatics.com Wed Mar 16 20:15:18 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 16 Mar 2005 20:15:18 -0500 Subject: [BiO BB] random sequences In-Reply-To: <200503161705.49792.jstroud@mbi.ucla.edu> References: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> <200503161705.49792.jstroud@mbi.ucla.edu> Message-ID: <4238DA26.3070300@scalableinformatics.com> I guess the question is random sequences, or sequences which preserve observed base probabilities, or pair probabilities, or ... There was a discussion about this here while ago. James Stroud wrote: > Python can do this with about 5 lines if you don't have a polynomial > distribution and about 8 if you do. Download and install python and run this > program (you will need to consult the manual to figure out how to run python > programs--pretty easy though). Work through the "hello world" example to get > started, then run the following program. > > > from random import choice > > seq_len = 100 > choices = ("A","T","G","C") > > the_seq = "" > for abase in xrange(seq_len): > the_seq += choice(choices) > > print the_seq > > > > If you have polynomial distributions, its a little more complicated > > James > > > On Monday 14 March 2005 10:46 am, Seema Trivedi wrote: > >>Dr. Boris Steipe, >>I will be highly obliged if you could kindly let me know if there are any >>softwares which I can use for generation of random sequences of >>nucleotides. I need to do this with large sequences. Thank you >>Sorry for the trouble, >>seema > > -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 From kanagasa at i2r.a-star.edu.sg Wed Mar 16 21:04:43 2005 From: kanagasa at i2r.a-star.edu.sg (K. Rajaraman) Date: Thu, 17 Mar 2005 10:04:43 +0800 (SGT) Subject: [BiO BB] random sequences In-Reply-To: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> Message-ID: Hi, Have you tried, http://rsat.ulb.ac.be/rsat/ On the left menu, under 'Other tools', click 'random sequence'. This tool allows you to create random sequences off the web. You can specify base probabilities, or you can generate using a Markov chain. -Raja --------------------------------------------------------------------- I2R, Singapore email: kanagasa at i2r.a-star.edu.sg --------------------------------------------------------------------- On Tue, 15 Mar 2005, Seema Trivedi wrote: [NON-Text Body part not included] From boris.steipe at utoronto.ca Wed Mar 16 23:10:36 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 16 Mar 2005 23:10:36 -0500 Subject: [BiO BB] random sequences In-Reply-To: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> Message-ID: <83A17B6A-969A-11D9-B9E8-000A9577512E@utoronto.ca> Hi Seema, On Monday, Mar 14, 2005, at 13:46 Canada/Eastern, Seema Trivedi wrote: > Dr. Boris Steipe, > I will be highly obliged if you could kindly let me know if there are > any softwares which I can use for generation of random sequences of > nucleotides. Yes , I had posted some teaching code here some time ago, attached below. Raja makes a good point about RSAT though: when you do any kind of statistics you should think carefully about what kind of "random" you want (and RSAT offers some nice options). Equiprobable nucleotides (like in the python code) are a poor random model for genetic sequences from organisms with high GC content. Independent single nucleotides are a poor random model for coding sequence; these would be better modelled from randomly chosen codons, weighted by amino acid frequencies, etc. I like to use the following principle: try to generate your random model so that it represents as much of what you already know as possible. Then a deviation from the model is due to something which is yet to be discovered. Good luck. Boris > I need to do this with large sequences. > Thank you > Sorry for the trouble, > seema > Disclaimer: this is *Teaching code* and could be written much more concisely. But that's not the point :-) ================================================================ #!/usr/bin/perl # # This program defines a number of Events, e.g. nucleotides # or amino acids or characters. Then frequencies are defined for each # of the events. Frequencies are converted into probabilities and # probabilities into cumulative intervals. # # Eg: Frequencies A: 4, C: 3, G: 2, T: 1 # Probabilities A: 0.4, C: 0.3, G: 0.2, T: 0.1 # Intervals A: 0.4 C: 0.7, G: 0.9, T: 1.0 # # This can be pictured like # # 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 # +----+----+----+----+----+----+----+----+----+----+ # | A | C | G | T | # +----+----+----+----+----+----+----+----+----+----+ # # .. now all we need to do is generate a random number between 0 and 1 # and see in which interval it falls. This is then the Event we # have chosen. # B. Steipe, public domain # ===================================================================== use strict; use warnings; my $OutputLength = 1000; # set target length my @Events; # Stores the events my @Probabilities; # Stores the probability of each event initializeArrays(); for (my $i=0; $i < $OutputLength; $i++) { print getEvent(rand); } print "\n"; exit(); # ====== Subroutines ======================= # sub initializeArrays { my $Sum = 0; # Initialize the events array - we write this into the code in this example here # but the frequencies could also be the result of counting amino acids in a database # or nucleotides in a genome, or dinucleotides etc. # In this example we generate a skewed nucleotide composition of four # different nucleotides, but it could be any number of characters. $Events[0] = 'A'; $Probabilities[0] = 9; $Events[1] = 'G'; $Probabilities[1] = 21; $Events[2] = 'C'; $Probabilities[2] = 32; $Events[3] = 'T'; $Probabilities[3] = 45; # Convert the values of the probabilities array to the top boundaries # of intervals having widths proportional to their relative frequency. # Sum over all frequencies ... for (my $i=0; $i <= $#Probabilities; $i++) { $Sum += $Probabilities[$i]; } # Divide frequencies by Sum to get probabilities ... for (my $i=0; $i <= $#Probabilities; $i++) { $Probabilities[$i] /= $Sum; } # Calculate upper bounds of cumulative intervals # going from 0 to 1.0 ... for (my $i=1; $i <= $#Probabilities; $i++) { $Probabilities[$i] += $Probabilities[$i-1]; } return(); } # ========================================== sub getEvent { my ($RandomNumber) = @_; my $i=0; # Test which interval contains the RandomNumber ... # The index of the interval points to the Event we should choose. for ($i=0; $i <= $#Probabilities; $i++) { if ($Probabilities[$i] > $RandomNumber) { last; } } return($Events[$i]); } From letondal at pasteur.fr Thu Mar 17 02:35:09 2005 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 17 Mar 2005 08:35:09 +0100 Subject: [BiO BB] random sequences In-Reply-To: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> References: <000601c528c6$2be46070$f7a0d6d2@semz03dtvn7b20> Message-ID: <994baaf0dd142e9c16e2927a25e4da4e@pasteur.fr> On Mar 14, 2005, at 7:46 PM, Seema Trivedi wrote: > I will be highly obliged if you could kindly let me know if there are > any softwares which I can use for generation of random sequences of > nucleotides. I need to do this with large sequences. > Thank you > Sorry for the trouble, > seema > Hi, This is a tool to generate related random sequences according to a phylogenetic tree: http://bioweb.pasteur.fr/seqanal/interfaces/seqgen.html -- Catherine Letondal -- Institut Pasteur From svtrived at hotmail.com Thu Mar 17 13:49:36 2005 From: svtrived at hotmail.com (Seema Trivedi) Date: Fri, 18 Mar 2005 00:19:36 +0530 Subject: [BiO BB] random sequences In-Reply-To: <200503161705.49792.jstroud@mbi.ucla.edu> Message-ID: Thanks for the information. seema >From: James Stroud >Reply-To: "The general forum at Bioinformatics.Org" > >To: "The general forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] random sequences >Date: Wed, 16 Mar 2005 17:05:49 -0800 > >Python can do this with about 5 lines if you don't have a polynomial >distribution and about 8 if you do. Download and install python and run >this >program (you will need to consult the manual to figure out how to run >python >programs--pretty easy though). Work through the "hello world" example to >get >started, then run the following program. > > >from random import choice > >seq_len = 100 >choices = ("A","T","G","C") > >the_seq = "" >for abase in xrange(seq_len): > the_seq += choice(choices) > >print the_seq > > > >If you have polynomial distributions, its a little more complicated > >James > > >On Monday 14 March 2005 10:46 am, Seema Trivedi wrote: > > Dr. Boris Steipe, > > I will be highly obliged if you could kindly let me know if there are >any > > softwares which I can use for generation of random sequences of > > nucleotides. I need to do this with large sequences. Thank you > > Sorry for the trouble, > > seema > >-- >James Stroud, Ph.D. >UCLA-DOE Institute for Genomics and Proteomics >Box 951570 >Los Angeles, CA 90095 >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Expressions unlimited! http://server1.msn.co.in/sp04/messenger/ The all new MSN Messenger! From vetdebarshi at gmail.com Thu Mar 17 13:26:41 2005 From: vetdebarshi at gmail.com (debarshi roy) Date: Thu, 17 Mar 2005 12:26:41 -0600 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 5, Issue 13 In-Reply-To: <1110945919.4237b07f70018@hongyu.org> References: <20050312170304.CB993D1F69@www.bioinformatics.org> <1110945919.4237b07f70018@hongyu.org> Message-ID: <9590758050317102652745dbd@mail.gmail.com> Hi Dr.Jhang, At present I am doing classes on Biostatistics, could you specify the most Important parts of Biostat or software thats important in nrespect of Bioinformatics? Presently I am using SAS. and what are the things in Algorithm development?Are you mentioning the Algebra or Calculas parts of mathematics? Thanks for your suggestion., Bye. Debarshi Roy. On Tue, 15 Mar 2005 20:05:19 -0800, Hongyu Zhang wrote: > > > The -m flag is cosmetic. The alignments you see are still pairwise > > alignments to the query sequence, not a multiple alignment. -m 1 > > Iddo, I agree to most of your points, however, since PSI-BLAST uses > the PSSM (Position Specific Score Matrix), I would argue that the > final alignment contains more than just a pair-wise alignment. PSSM > is built upon the multiple sequences aligned in the previous round of > iterations. > > > Could you please help me by providing with some basic informations? > > I would like to know aboput the prerequisite knowledge for > > Bioinformatics research What are computer programming language > > which > > are of most importance? > > and what are the lab techniques needed ? > > Hi Deharshi. C/C++, Java and Perl are most important languages in > bioinformatics. C/C++ is more popular on speed sensitive > applications, while Java and Perl are more popular on database and > web related applications. C# is also catching up recently. In > addition to computer languages, you should take some classes on > algorithm development and statistics, which will make you more than > just a bioinformatics programmer. > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From moyc at mail.med.upenn.edu Fri Mar 18 15:47:54 2005 From: moyc at mail.med.upenn.edu (Chris Moy) Date: Fri, 18 Mar 2005 15:47:54 -0500 Subject: [BiO BB] Function Search Message-ID: <00AAA9EA-97EF-11D9-AC8C-000A9599E70C@mail.med.upenn.edu> Hello All, I am in the process of trying to mine some of the data to see if there is a possible function for a protein of interest. I have been performing PSI-Blast with a whole set of organisms and the process is quickly becoming a little overwhelming in terms of trying to make sense of all the data. Does anyone have any suggestions about a systematic way to get a handle on possible functions for a region of my protein. Right now I have limited my search to 300 residues that are just a small portion of the protein of interest. Suggestions regarding the use of HMMRs and PSSMs are welcome! Chris Chris Moy University of Pennsylvania - Department of Ophthalmology/Genetics 215-898-9838 moyc at mail.med.upenn.edu From danny at amelang.net Fri Mar 18 16:07:54 2005 From: danny at amelang.net (Daniel Amelang) Date: Fri, 18 Mar 2005 14:07:54 -0700 Subject: [BiO BB] Function Search In-Reply-To: <00AAA9EA-97EF-11D9-AC8C-000A9599E70C@mail.med.upenn.edu> References: <00AAA9EA-97EF-11D9-AC8C-000A9599E70C@mail.med.upenn.edu> Message-ID: <423B432A.7040704@amelang.net> This is one of the first options to come to mind. And one of the more popular. http://hmmer.wustl.edu/ http://pfam.wustl.edu/hmmsearch.shtml Dan Chris Moy wrote: > Hello All, > > I am in the process of trying to mine some of the data to see if there > is a possible function for a protein of interest. I have been > performing PSI-Blast with a whole set of organisms and the process is > quickly becoming a little overwhelming in terms of trying to make > sense of all the data. Does anyone have any suggestions about a > systematic way to get a handle on possible functions for a region of > my protein. Right now I have limited my search to 300 residues that > are just a small portion of the protein of interest. Suggestions > regarding the use of HMMRs and PSSMs are welcome! > > Chris > > > > Chris Moy > University of Pennsylvania - Department of Ophthalmology/Genetics > 215-898-9838 > moyc at mail.med.upenn.edu > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From penghanchuan at yahoo.com Sat Mar 19 19:47:23 2005 From: penghanchuan at yahoo.com (Hanchuan Peng) Date: Sat, 19 Mar 2005 16:47:23 -0800 (PST) Subject: [BiO BB] Call for Papers and Participation: Int. Workshop on "BioImage Data Mining and Informatics", Stanford, CA, Aug 12, 2005. in conjuction with CSB 2005 Message-ID: <20050320004723.8121.qmail@web41522.mail.yahoo.com> International Workshop on "BioImage Data Mining and Informatics" Call for Papers and Participation Stanford, CA ?C August 12, 2005 Sponsored by IEEE Technical Committee on Bioinformatics Papers are solicited for a workshop on bioimage data mining and image analysis to solve bioinformatics and biomedicine problems. This workshop is in conjunction with CSB2005, the IEEE Computational Systems Bioinformatics conference, Stanford, CA, Aug. 8?C12, 2005. With the development of advanced imaging techniques, the number of biological images (e.g. cellular and molecular images, as well as medical images) acquired in digital forms is growing rapidly. Large-scale bioimage databases are becoming available. Analyzing these images sheds new light for biologists to seek answers to many biological problems. For example, analysis of the spatial distribution of proteins in molecular images can differentiate cancer cell phenotypes. Comparison of in situ gene expression pattern images during embryogenesis helps to delineate the underlying gene networks. Image analysis related techniques (e.g. wavelet) have also been found useful in bioinformatics problems such as sequence analysis. The potential of mining the information in bioimages to answer biological questions is enormous and it cries for advanced techniques of bioimage data mining and informatics. As a prompt response to this call, the goal of this workshop is to bring together interdisciplinary researchers to identify problems and present answers to bioimage data mining and informatics using cutting edge image data analysis, computer vision, data mining, machine learning, and informatics methods. Papers addressing issues of data mining and informatics, related to bioimages, are welcome. Appropriate topics include but are not limited to: * Acquisition of cellular, molecular and other bioimages; novel bioimaging techniques; novel bioimage data * Bioimage feature measurement, description, extraction, and selection * Bioimage registration and comparison * Object segmentation and tracking in bioimages * Clustering/classification of bioimages or patterns derived from bioimages * Object/pattern recognition and understanding in bioimages * Bioimage ontology and related data mining * Bioimage data visualization * Other bioimaging related techniques, including transmission, compression, storage, database, etc. * Tools/software for bioimage data processing and data mining * Bioimage related biology, bioinformatics, and biomedicine applications, e.g. 3D protein structure reconstruction, protein structure analysis and prediction, gene regulatory network/pathway modeling, etc. * Microarray image analysis and data mining * Joint analysis using both bioimages and other data (e.g. sequences, microarray, protein interaction, etc.) * Other bioinformatics problems where image pattern analysis, signal processing, and computer vision methods can be applied. Extended abstracts of 4 to 6 pages in length, or full papers, should be emailed to Dr. Fuhui Long (flong at lbl.gov) and Dr. Hanchuan Peng (hpeng at lbl.gov) at the Lawrence Berkeley National Laboratory, University of California, Berkeley, no later than April 17, 2005. The abstracts and papers will be peer-reviewed. Accepted papers will be included in the conference Proceedings of the IEEE CSB 2005 published by IEEE Computer Society Press. The final versions of accepted papers are limited to 10 pages in IEEE conference format (will be emailed to the respective authors). Talk proposals with a short abstract, but without full papers, are also welcome. These abstracts will be included in the workshop program as well. Important dates for paper submissions: * April 17, 2005 - extended abstract due * April 30, 2005 - notification of acceptance/rejection * May 22, 2005 - final paper/abstract due Questions should be sent to the workshop organizers at flong at lbl.gov and hpeng at lbl.gov. Show your support for an IEEE Life Sciences Society. Sign up now: http://lifesciencessociety.org/proposal_support.php From frcerqueira at gmail.com Wed Mar 23 19:01:11 2005 From: frcerqueira at gmail.com (Fabio Cerqueira) Date: Wed, 23 Mar 2005 21:01:11 -0300 Subject: [BiO BB] free software for clustering Message-ID: <50fceb2c0503231601363136a7@mail.gmail.com> Hi, does anyone know a free software for clustering? Thanks, . Fabio . From idoerg at burnham.org Wed Mar 23 19:46:53 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 23 Mar 2005 16:46:53 -0800 Subject: [BiO BB] free software for clustering In-Reply-To: <50fceb2c0503231601363136a7@mail.gmail.com> References: <50fceb2c0503231601363136a7@mail.gmail.com> Message-ID: <42420DFD.6090705@burnham.org> Fabio Cerqueira wrote: >Hi, > >does anyone know a free software for clustering? > >Thanks, > > . Fabio . >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > Cluto http://www-users.cs.umn.edu/~karypis/cluto/ R http://r-project.org Weka http://www.cs.waikato.ac.nz/~ml/weka/ ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo ========================== The First Automated Protein Function Prediction SIG Detroit, MI June 24, 2005 http://ffas.burnham.org/AFP From idoerg at burnham.org Wed Mar 23 19:48:24 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 23 Mar 2005 16:48:24 -0800 Subject: [BiO BB] free software for clustering In-Reply-To: <50fceb2c0503231601363136a7@mail.gmail.com> References: <50fceb2c0503231601363136a7@mail.gmail.com> Message-ID: <42420E58.8050905@burnham.org> See also: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/index.html Fabio Cerqueira wrote: >Hi, > >does anyone know a free software for clustering? > >Thanks, > > . Fabio . >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 http://ffas.ljcrf.edu/~iddo ========================== The First Automated Protein Function Prediction SIG Detroit, MI June 24, 2005 http://ffas.burnham.org/AFP From deepan_3356 at yahoo.co.in Thu Mar 24 01:22:34 2005 From: deepan_3356 at yahoo.co.in (deepan@bioinformatics.org) Date: Thu, 24 Mar 2005 06:22:34 +0000 (GMT) Subject: [BiO BB] free software for clustering In-Reply-To: 6667 Message-ID: <20050324062234.31068.qmail@web8401.mail.in.yahoo.com> MOSIX LAM where the popular free clustering software but i think there are better thing now ..if u are not able to find the latest one.. remind me i shall locate it and tell u.. bye the what is the program that u want to run in the cluster.. regards deepan --- Iddo Friedberg wrote: > See also: > > http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/index.html > > > Fabio Cerqueira wrote: > > >Hi, > > > >does anyone know a free software for clustering? > > > >Thanks, > > > > . Fabio . > >_______________________________________________ > >Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 USA > Tel: +1 (858) 646 3100 x3516 > http://ffas.ljcrf.edu/~iddo > ========================== > The First Automated Protein Function Prediction SIG > Detroit, MI June 24, 2005 > http://ffas.burnham.org/AFP > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > my home page http://deepan.tk mail id : deepan at bioinformatics.org ----------------------------------------- deepan chakravarthy n 3rd year,(5th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: home:04287-241199,04287-244399, brother no:9840824399, address: ac tech hostel (jh 108), anna university, chennai-25. Send instant messages to your online friends http://uk.messenger.yahoo.com From DGURGUL at PARTNERS.ORG Thu Mar 24 09:12:24 2005 From: DGURGUL at PARTNERS.ORG (Gurgul, Dennis J.) Date: Thu, 24 Mar 2005 09:12:24 -0500 Subject: [BiO BB] free software for clustering Message-ID: <11821FC5155A5A48AB5CF6480C46D864B7F135@PHSXMB1.partners.org> Been using Rocks for years with minimal problems: http://rocks.npaci.edu/Rocks/ Also, OSCAR, uses systemimager: http://oscar.openclustergroup.org/tiki-index.php Dennis J. Gurgul Research Computing Partners Health Care 617.724.3169 http://www.partners.org/rescomputing -----Original Message----- From: bio_bulletin_board-bounces+dgurgul=partners.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+dgurgul=partners.org at bioinformatics.o rg]On Behalf Of Fabio Cerqueira Sent: Wednesday, March 23, 2005 7:01 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] free software for clustering Hi, does anyone know a free software for clustering? Thanks, . Fabio . _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From thomas_tunney at yahoo.com Thu Mar 24 16:01:04 2005 From: thomas_tunney at yahoo.com (thomas tunney) Date: Thu, 24 Mar 2005 13:01:04 -0800 (PST) Subject: [BiO BB] CrimeStat Spatial Statistics Program Message-ID: <20050324210104.8035.qmail@web53704.mail.yahoo.com> I'm not sure this will help, but it may: http://www.icpsr.umich.edu/NACJD/crimestat.html This program was originally prepared under the auspices of the National Institute of Justice to analyze crime data on Geographic Information Systems for police agencies, but it will work with any kind of point data (and presumably any kind of vector space, as well as GIS layers). It is especially good at mapping first order 'hot spots' (clusters) and second order 'hot spots' (clusters of clusters). You can download Version 2.0 for free from the site indicated above. Bonne chance! --Thomas C. Tunney --------------------------------- Do you Yahoo!? Yahoo! Small Business - Try our new resources site! -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.gille at charite.de Wed Mar 30 10:21:12 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 30 Mar 2005 17:21:12 +0200 (CEST) Subject: [BiO BB] endoplas reticulum Message-ID: <45347.192.168.220.204.1112196072.squirrel@webmail.charite.de> Does anybody know a list of proteins that exist within the ER in human or mammals ? Many thanks From bassis at dsi.unimi.it Wed Mar 30 10:37:16 2005 From: bassis at dsi.unimi.it (Simone Bassis) Date: Wed, 30 Mar 2005 17:37:16 +0200 Subject: [BiO BB] NAIS'05 Int. Workshop - Extended Deadline Message-ID: <200503301737.16911.bassis@dsi.unimi.it> Dear Colleagues (Apologies if you receive this more than once), To accommodate those not quite finished but hoping to submit enough time to complete their papers, we have agreed to extend the deadline for submission by two weeks until friday April 15, 2005. Depending on their content, refereed extended versions of selected paper will be published on a special issue of either Natural Computing or Nonlinear Analysis C-series. Kind Regards, Organizing Committee ================= Call for Papers International Workshop on Natural and Artificial Immune Systems (NAIS 2005) Vietri sul Mare, Salerno, Italy, June 9-10, 2005 http://siren.dsi.unimi.it/conferences/IMMUNE05/html/index.html * Venue International Institute For Advanced Scientific Studies (IIASS), "E.R.Caianiello", Vietri sul Mare, (SA) Italy. http://www.iiassvietri.it/index.html http://www.iiassvietri.it/school2004/ * Important Dates Submission deadline: April 15 2005 Acceptance/Rejection notification: May 2, 2005 Camera-ready copy of papers: June 6, 2005 Workshop Date: June 9-10, 2005 * Aims and Scope The workshop aims at catalyzing the interaction between modelers (computer scientists, mathematicians and physicists), immunologists and biologists interested in discussing the information processing mechanisms emerging in the functionalities of either natural or artificial immune systems. The leading idea motivating this event is the attention to the various forms of ?intelligent thinking? underlying the many attack/defense/adaptation strategies discovered in natural systems, such as tumor and virus escape mechanisms of animals and humans, or implemented in artificial systems. This approach may reap several basic benefits of the original cybernetics paradigm: -the emergence of the mind from chemical-physical reactions that can be studied and simulated, - the use of natural processing mechanisms for solving artificial problems, and the cross-fertilization of the natural and artificial research environments, -the adoption of comprehensive immune system models in the development of new therapeutic approaches. Possible topics include, but are not limited to: # Computational Immunology # Immunological Computation # Immunoinformatics # modelling and simulation of immune systems # model testing and game theory # biological and immersive learning # network security and artificial virus attacks # comparisons between Artificial Immune Systems and other biologically-inspired paradigms # theory and applications of Immunological Computing # Immunocomputing * Invited speakers - Franco Celada, University of Genova, Italy - Vincenzo Cutello, University of Catania, Italy - Dipankar Dasgupta, University of Memphis, USA - Doheon Lee, IBM-KAIST Bio-Computing Research Center, Korea - Jon Timmis, Universityh of Kent, UK * Conference Proceedings The conference will feature both introductory tutorials and original refereed papers, to be published by an international publisher. See details of electronic submission on the web page: http://siren.dsi.unimi.it/conferences/IMMUNE05/html/index.html Depending on their content, refereed extended versions of selected paper will be published on a special issue of either Natural Computing or Nonlinear Analysis C-series. * Conference Chairs: - Bruno Apolloni, University of Milano, Italy. apolloni at dsi.unimi.it - Alberto Clivio, University of Milano, Italy. alberto.clivio at unimi.it - Vincenzo Cutello, University of Catania, Italy. cutello at dmi.unict.it - Giuseppe Nicosia, University of Catania, Italy. nicosia at dmi.unict.it *Programme Committee: - Franco Celada, University of Genova, Italy - Dipankar Dasgupta, University of Memphis, USA - Marco Gori, University of Siena, Italy - Doheon Lee, IBM-KAIST Bio-Computing Research Center, Korea - Piero Mussio, University of Milano, Italy - Anastasia Pagnoni, Unversity of Milano, Italy - Jon Timmis, Universityh of Kent, UK - Henry Linger, Monash University, Melbourne, Australia - Fernando Esponda, University of New Mexico, USA * Getting Vietri Sul Mare http://www.iiassvietri.it/school2004/getting_vietri.htm * NAIS 2005 Conference Secretariats: - Department of Mathematics and Computer Science University of Catania, City University, V.le A. Doria 6, 95125 Catania, Italy Email: nais05 at dmi.unict.it Phone: +39-095-7383074 Fax: +39-095-330094 or - Dip. di Scienze Dell'Informazione. University of Milano Via Comelico, 39 20125 Milano, Italy Email: bassis at dsi.unimi.it Phone: +39-02-50316335 Fax: +39-02-50316228 * For additional information or questions, contact Alberto Clivio, University of Milano, Italy, alberto.clivio at unimi.it Giuseppe Nicosia, University of Catania, Italy, nicosia at dmi.unict.it -- Giuseppe Nicosia Ph.D. in Computer Science Department of Mathematics and Computer Science University of Catania V.le A. Doria 6 - 95125 Catania, Italy Email: nicosia at dmi.unict.it Tel: + 39 095 738 30 80 Fax: + 39 095 33 00 94 Web: www.dmi.unict.it/~nicosia From logan at cacs.louisiana.edu Wed Mar 30 11:58:11 2005 From: logan at cacs.louisiana.edu (logan at cacs.louisiana.edu) Date: Wed, 30 Mar 2005 10:58:11 -0600 (CST) Subject: [BiO BB] Call for Participation Message-ID: <2559.68.226.154.226.1112201891.squirrel@webmail.cacs.louisiana.edu> Place: Lafayette, Louisiana Date: April 18, 2005 Paper due: March 18, 2005 Symposium web site: http://www.cacs.louisiana.edu/bioinformatics/symp05/index.html The registration is open for the Second Annual Bioinformatics Symposium 2005. The symposium's goal is to build a bridge among the researchers working in industries, academic and research institutions. This forum will provide an opportunity to learn and to understand the ongoing research activities that may help spark some new collaboration for future research and funding opportunities in this area. Keynote Speakers include: Professor Philip E. Bourne from UCSD Co-Director Protein Data Bank, Topic: Recent Developments in Structural Bioinformatics Professor. Ed Seidel from Center for Computation & Technology, Louisiana State University Topic: Grid Computing Dr. Mark Gosink, Head of Computational Biology of Scripps Florida Topic: Informatics at Scripps Florida Participation: Registration ($25 for students and $50 for others) is required to attend the symposium. The registration fee allows you to attend all the sessions, breakfast, lunch and two cofee breaks. On line registration is opened while seats are available. Thank you for your time Raja Logananatharaj Bioinformatics Symposium Organizer From deletto at unisa.it Thu Mar 31 09:56:25 2005 From: deletto at unisa.it (Davide Eletto) Date: Thu, 31 Mar 2005 16:56:25 +0200 Subject: [BiO BB] 3D Protein structure prediction In-Reply-To: <005301c52428$e0cf4920$0401a8c0@atarippc> References: <20050307175121.64738.qmail@web61301.mail.yahoo.com> <422DB84D.5060907@unisa.it> <005301c52428$e0cf4920$0401a8c0@atarippc> Message-ID: <424C0F99.3080707@unisa.it> Hi all, please sorry for bothering you with a so trivial question. Anyone of you have any idea about the possibility to retrieve a 2ndary and/or 3ry protein structure from a simple aminoacids sequence? I mean, moreover, there is anywhere a tool that works comparing the query sequence against a domains database, and gives a results of % identity? Many thanks in advance. Bye davide From yqzhou at buffalo.edu Thu Mar 31 10:09:18 2005 From: yqzhou at buffalo.edu (Yaoqi Zhou) Date: Thu, 31 Mar 2005 10:09:18 -0500 Subject: [BiO BB] 3D Protein structure prediction In-Reply-To: <424C0F99.3080707@unisa.it> References: <20050307175121.64738.qmail@web61301.mail.yahoo.com> <422DB84D.5060907@unisa.it> <005301c52428$e0cf4920$0401a8c0@atarippc> <424C0F99.3080707@unisa.it> Message-ID: <85150fcddf6f1ae0013249bda4b32d78@buffalo.edu> Try SP^3 at http://theory.med.buffalo.edu Yaoqi Zhou, Associate Professor **CHECK out Newly UPDATED webpage** Department of Physiology and Biophysics University at Buffalo, State University of New York 124 Sherman Hall, Buffalo, NY 14214 (716) 829-2985 Fax (716) 829-2344 Email: yqzhou at buffalo.edu NEW Office/Lab Address: 306/308 Cary Hall http://theory.med.buffalo.edu On Mar 31, 2005, at 9:56 AM, Davide Eletto wrote: > Hi all, > please sorry for bothering you with a so trivial question. > > Anyone of you have any idea about the possibility to retrieve a 2ndary > and/or 3ry protein structure from a simple aminoacids sequence? I > mean, moreover, there is anywhere a tool that works comparing the > query sequence against a domains database, and gives a results of % > identity? > > Many thanks in advance. > > Bye > davide > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From kalita at rabbit.uccs.edu Thu Mar 31 13:57:59 2005 From: kalita at rabbit.uccs.edu (J. Kalita) Date: Thu, 31 Mar 2005 11:57:59 -0700 (MST) Subject: [BiO BB] BIOT-05 papers and abstracts due In-Reply-To: <20050331170506.00C3FD1F53@www.bioinformatics.org> References: <20050331170506.00C3FD1F53@www.bioinformatics.org> Message-ID: <52346.128.198.172.116.1112295479.squirrel@128.198.172.116> Papers and abstracts in all aspects of Bioinformatics and Biotechnolgy are officially due today (3/31/05). The symposium features peer-reviewed papers that are presetend orally or in poster sessions. Extended abstracts (2 pages long) or full papers (up to 6 pages long) are requested. Please visit the http://bioinfo.uccs.edu and click on "Symposium 2005 (BIOT-05)". The symposium will be held in Colorado Springs, Colorado on August 15th and 16th. We had a very successful symposium in 2004. There was a printed proceedings document with all the accepted abstracts and papers. The printed proceedings are available on-line at the http://bioinfo.uccs.edu Web site. Please go to the Web site and submit your extended abstract or paper as soon as possible. If you want a little extra time (say, up to an extra week), please write to me. Jugal Kalita Department of Computer Science University of Colorado at Colorado Springs PS: We are looking for any other universities or organizations (in the US or Canada) that want to be co-sponsors of this symposium. We can hold it in several locations in alternate yers.