From Nadia.Bolshakova at cs.tcd.ie Tue Jan 4 06:19:39 2005 From: Nadia.Bolshakova at cs.tcd.ie (Nadia Bolshakova) Date: Tue, 4 Jan 2005 11:19:39 -0000 Subject: [BiO BB] Call for Special Track "BIOINFORMATICS and its MEDICAL APPLICATIONS" Message-ID: <026d01c4f24f$480df930$6e26e286@DBNJK90J> The 18th IEEE Symposium on Computer-Based Medical Systems Special Track: BIOINFORMATICS and its MEDICAL APPLICATIONS http://www.cs.tcd.ie/Nadia.Bolshakova/CBMS_Bioinformatics.html CALL FOR PAPERS Major computational challenges have been raised in the post-genomic era. Novel computational methods and approaches are required to acquire, store, organize, archive, analyse and visualize the large amount of biological and biomedical data. The goal of the track is to share ideas related to bioinformatics challenge among biological, biomedical and computer scientists. Authors are invited to submit original papers addressing any computational biology issue. Papers are invited (but not limited) to the following key themes: Biomedical Research Evolution and Phylogenetics Data Mining in Bioinformatics Microarray Analysis RNAi Analysis Sequence Alignment Pathways, Networks, Systems Biology Functional Genomics Visualization Protein Structure and Analysis Comparative Genomics Pattern Recognition Software Systems IMPORTANT DATES January 26, 2005 - Submission of (6-page, maximum) paper March 1, 2005 - Notification of acceptance March 24, 2005 - Final camera-ready paper due March 24, 2005 - Pre-registration deadline You must pre-register to have your paper published in the proceedings. If you only plan to attend and are not submitting a paper, pre-registration is still strongly encouraged. This conference is space-limited, and registration may not be available on-site. SUBMISSION PROCEDURES FOR PAPER No hardcopy submissions are being accepted. Electronic submissions of original technical research papers will only be accepted in PDF format. File size is limited to 2 MB. Use a maximum of six A4 pages, including figures and references. Include one cover sheet, stating the paper title, authors, technical area(s) covered in the article, corresponding author's information (telephone, fax, mailing address, e-mail address), and your preference for oral or poster presentation. Author names should appear only on the cover sheet, not on the summary. Submit your manuscript no later than January 26, 2005. Authors will be notified of acceptance by March 1, 2005 after a review process by three independent experts. Each accepted paper will be published in the conference proceedings by IEEE CS Press, conditional upon the author's advance registration. Submission in the IEEE Computer Science Press 6x9-inch format is encouraged. Formatting instructions, LaTeX macros and MSWord templates are available at ftp://pubftp.computer.org/press/outgoing/proceedings. Authors should indicate the special track title (on the cover sheet). All submissions should be done electronically via the IEEE CBMS 2005 web submission system at: http://www.cs.tcd.ie/research_groups/mlg/CBMS2005/openconf. TRACK CHAIR Nadia Bolshakova -Trinity College Dublin, Ireland TRACK PROGRAM COMMITTEE Francisco Azuaje - University of Ulster, Northern Ireland Joaqu?n Dopazo - Centro Nacional de Investigaciones Oncol?gicas, Spain Mario A. Fares -NUI Maynooth, Ireland Des Higgins -University College Dublin, Ireland Fernando Martin-Sanchez -Institute of Health "Carlos III", Spain Manolis Tsiknakis - Foundation for Research and Technology-Hellas, FORTH, Greece For further questions, please contact Nadia.Bolshakova at cs.tcd.ie -------------- next part -------------- An HTML attachment was scrubbed... URL: From carlosandresic at yahoo.com.mx Wed Jan 5 15:36:32 2005 From: carlosandresic at yahoo.com.mx (Carlos Iriarte) Date: Wed, 5 Jan 2005 15:36:32 -0500 (EST) Subject: [BiO BB] Invitation Message-ID: <311754.1104957521171.JavaMail.root@nelson> Carlos Iriarte has invited you to join hi5. By joining hi5, you will be connected to Carlos and all of Carlos's friends. hi5 is the place where friends meet. You can use hi5 for the following purposes: * Find old friends * Meet new people * Browse photos Join Carlos, meet Carlos's friends, and meet people that share your interests now! Click here: http://www.hi5.com/splash/HDJGL?inviteId=ZCYQN18EAM6784588b138904057 This invitation was sent to bio_bulletin_board at bioinformatics.org on behalf of Carlos Iriarte (carlosandresic at yahoo.com.mx). If you do not wish to receive invitations from hi5 members, click on the link below: http://www.hi5.com/friend/displayBlockInvite.do?inviteId=138904057 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hepu.deng at rmit.edu.au Wed Jan 5 19:29:01 2005 From: hepu.deng at rmit.edu.au (Hepu Deng) Date: Thu, 06 Jan 2005 11:29:01 +1100 Subject: [BiO BB] ICNC*05-FSKD*05 Call for Papers: Changsha China Message-ID: ---------------------------------------------------------------------- 2005 International Conference on Natural Computation (ICNC'05) International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'05) ---------------------------------------------------------------------- 27 - 29 August 2005, Changsha, China ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home Page: http://www.xtu.edu.cn/nc2005 http://www.ntu.edu.sg/home/elpwang/nc2005 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *** Submission Deadline: 15 March 2005 *** CALL FOR PAPERS The 2005 International Conference on Natural Computation (ICNC? 05) and the 2005 International Conference on Fuzzy Systems and Knowledge Discovery (FSKD? 05) will be jointly held in Changsha, China from 27 - 29 August 2005. The conferences will feature the most up-to-date research results in computational algorithms inspired from nature, including biological, ecological, and physical systems. It is an exciting and emerging interdisciplinary area in which a wide range of techniques and methods are being studied for dealing with large, complex, and dynamic problems. Specific areas include neural computation, evolutionary computation, quantum computation, DNA computation, chemical computation, information processing in cells and tissues, molecular computation, computation with words, fuzzy computation, granular computation, artificial life, swarm intelligence, ants colony, artificial immune systems, etc., with applications to knowledge discovery, finance, operations research, and more. The joint conferences will also promote cross-fertilization over these exciting and yet closely-related areas. Registration to either conference will entitle a participant to the proceedings and technical sessions of both conferences, as well as the conference banquet and meals. Publications: ------------ The ICNC? 05 and FSKD'05 conference proceedings will be published in Springer-Verlag? s Lecture Notes in Computer Science (LNCS) and Lecture Notes in Artificial Intelligence (LNAI), respectively. Both the LNCS and LNAI are indexed in SCI-Expanded. A selected number of authors will be invited to expand and revise their papers for possible inclusions in peer-reviewed international journals / edited books. About Changsha, Hunan, China: ---------------------------- Changsha, the capital of Hunan Province, is a historic and cultural city in southern China and a busy port on the Xiangjiang River, with a population over 6 million. Founded 3000 years ago, the city became the capital of the Zhou state (951-960 AD) and a leading commercial center during the Song dynasty (960-1279 AD). Changsha International Airport is easily accessible with direct flights to all major domestic and some international destinations. Other famous tourist destinations in Hunan include the Zhangjiajie National Park (natural heritage listed by UN) and Fenghuang (Phoenix) Ancient City. Important Dates --------------- Paper Submission Deadline: 15 March 2005 Notification of Acceptance: 15 April 2005 Camera-Ready Copy Due: 15 May 2005 Contact ------- Email: nc2005 at xtu.edu.cn Phone/Fax: +86 732 829 2201 / 829 3249 Submission of Papers -------------------- Authors are invited to submit a full paper as an electronic file (postscript, pdf or Word format) at the conference website. Templates are available at the Springer website. Sponsorship / Exhibition ------------------------ The conferences will offer product vendors a sponsorship package and/or an opportunity to interact with conference participants. Product demonstration and exhibition can also be arranged. For more information, please visit the conference web page. Sponsor / Organizer ------------------- Xiangtan University, China Technical Co-Sponsor -------------------- IEEE Circuits and Systems Society In Co-operation with -------------------- International Neural Network Society Chinese Association for Artificial Intelligence European Neural Network Society Fuzzy Mathematics and Systems Association of China Japanese Neural Network Society Asia-Pacific Neural Network Assembly Honorary Conference Chairs -------------------------- Shun-ichi Amari, Japan Lotfi A. Zadeh, USA International Advisory Board ---------------------------- Toshio Fukuda, Japan Kunihiko Fukushima, Japan Tom Gedeon, Australia Aike Guo, China Zhenya He, China Janusz Kacprzyk, Poland Nik Kasabov, New Zealand John A. Keane, UK Soo-Young Lee, Korea Erkki Oja, Finland Nikhil R. Pal, India Witold Pedrycz, Canada Jose Principe, USA Harold Szu, USA Shiro Usui, Japan Xindong Wu, USA Lei Xu, Hong Kong, China Xin Yao, UK Syozo Yasui, Japan Bo Zhang, China Yixin Zhong, China Jacek M. Zurada, USA General Chair ------------- He-An Luo, China General Co-Chairs ----------------- Lipo Wang, Singapore Yunqing Huang, China Program Chairs -------------- ICNC? 05: Ke Chen, UK Yew Soon Ong, Singapore FSKD? 05: Yaochu Jin, Germany Local Arrangement Chairs ------------------------ Renren Liu, China Xieping Gao, China Proceedings Chair ----------------- Fen Xiao, China Publicity Chair --------------- Hepu Deng, Australia Sponsorship/Exhibits Chair -------------------------- Shaoping Ling, China Webmaster --------- Linai Kuang, China From MAG at Stowers-Institute.org Mon Jan 10 14:47:03 2005 From: MAG at Stowers-Institute.org (Goel, Manisha) Date: Mon, 10 Jan 2005 13:47:03 -0600 Subject: [BiO BB] All-vs-All Global protein seq alignment score Message-ID: <20050110194439.3308DD1F15@www.bioinformatics.org> Hi All, I have a database of about 400 squences, which I want to compare All-vs-All to get the global alignment score of each protein sequence pair. I tried using bl2seq but that gives me local alignments. What other program would suit this function best ? I would probably like to have the flexibility of being able to use various matrices. Thanks a lot, -Manisha -------------- next part -------------- An HTML attachment was scrubbed... URL: From christoph.gille at charite.de Mon Jan 10 16:30:39 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 10 Jan 2005 22:30:39 +0100 (MET) Subject: [BiO BB] All-vs-All Global protein seq alignment score In-Reply-To: <20050110194439.3308DD1F15@www.bioinformatics.org> References: <20050110194439.3308DD1F15@www.bioinformatics.org> Message-ID: <32774.217.81.119.180.1105392639.squirrel@webmail.charite.de> Manisha, I have added this to the alignment program STRAP. Load all 400 sequences into the program. Chose from the menu analysis/ compare some sequences. chose table and not graph and select alignment score as a distance measure. click the hand icon to select an alignment procetdure like neobio or clustalw or whatever. Only those that provide a score can be used. And wait for the computation to be completed. The output is a flat text list. Before you analyse the 400 sequences try everything with 10 sequences. good luck Christoph > Hi All, > > > I have a database of about 400 squences, which I want to compare > All-vs-All to get the global alignment score of each protein sequence > pair. I tried using bl2seq but that gives me local alignments. > What other program would suit this function best ? > I would probably like to have the flexibility of being able to use > various matrices. > > Thanks a lot, > -Manisha > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From karplus at soe.ucsc.edu Mon Jan 10 15:31:33 2005 From: karplus at soe.ucsc.edu (Kevin Karplus) Date: Mon, 10 Jan 2005 12:31:33 -0800 Subject: [BiO BB] Re: pdb-l: All-vs-All Global protein seq alignment score In-Reply-To: <200501101947.j0AJlMR27795@postal.sdsc.edu> (MAG@Stowers-Institute.org) References: <200501101947.j0AJlMR27795@postal.sdsc.edu> Message-ID: <200501102031.j0AKVX2f004125@cheep.cse.ucsc.edu> I rarely have a need for global alignment (unless the proteins have been pre-trimmed to have matching domains, global alignment is usually over alignment), and I rarely have a need for all-vs-all alignment of single sequences (I get much better alignments by doing iterative search). If you are sure that you are working on the right problem, there are plenty of global aligners available. Almost all the standard tool suites include one. http://www.hku.hk/bruhk/sgaln.html contains a list of a few of the more common ones (found by googling global alignment , a task that I thought anyone who could send e-mail to these mailing lists was capable of). ------------------------------------------------------------ Kevin Karplus karplus at soe.ucsc.edu http://www.soe.ucsc.edu/~karplus Professor of Biomolecular Engineering, University of California, Santa Cruz Undergraduate and Graduate Director, Bioinformatics (Senior member, IEEE) (Board of Directors, ISCB) life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck (lapsed) Affiliations for identification only. From mycahya at fastmail.fm Mon Jan 10 23:16:06 2005 From: mycahya at fastmail.fm (Cahya Prihatna) Date: Mon, 10 Jan 2005 20:16:06 -0800 Subject: [BiO BB] (no subject) Message-ID: <1105416966.7172.212450112@webmail.messagingengine.com> -- Cahya Prihatna mycahya at fastmail.fm From christoph.gille at charite.de Tue Jan 11 10:07:48 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 11 Jan 2005 16:07:48 +0100 (MET) Subject: [BiO BB] DNA vectore design what software Message-ID: <38336.192.168.220.204.1105456068.squirrel@webmail.charite.de> The Charite of the Humboldt University of Berlin currently looks for good program for DNA vector design. Currently we take Vector NTI (www.invitrogen.com) and GENTLE into consideration. If there is any other program we should check out as well please tell me. Many thanks From forward at hongyu.org Tue Jan 11 13:01:14 2005 From: forward at hongyu.org (Hongyu Zhang) Date: Tue, 11 Jan 2005 10:01:14 -0800 Subject: [BiO BB] Re: All-vs-All Global protein seq alignment score Message-ID: <1105466474.41e4146a4972d@hongyu.org> What I usually do is a two-step method. First, I use a local alignment programs like BLAST to quickly detect those close relatives for each sequence; second, I use a global alignment program like ClustalW to align those close pairs to get a global score. If you just want to get all-vs-all Smith-Watermann alignment scores, then you just need one step: using WU-BLAST with -postsw flag. -- Hongyu Zhang Computational biologist Ceres Inc. From davidg at lsi.upc.edu Thu Jan 13 15:17:42 2005 From: davidg at lsi.upc.edu (=?iso-8859-1?Q?David_Garc=EDa_Cort=E9s?=) Date: Thu, 13 Jan 2005 21:17:42 +0100 Subject: [BiO BB] Problems parsing PSI-BLAST results References: <20050112170010.8E5B6D1F24@www.bioinformatics.org> Message-ID: <003e01c4f9ac$f34bf8b0$cf1e5393@Davidg> Hello. I'm trying to parse the hits of all the iterations in a PSI-BLAST result (which I have in a variable, not in a file), but I can't make it work. It gives me the following error: Use of uninitialized value in index at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Sbjct.pm line 271, line 54. Use of uninitialized value in length at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Sbjct.pm line 272, line 54. Use of uninitialized value in join or string at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Sbjct.pm line 283, line 54. Use of uninitialized value in join or string at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Sbjct.pm line 284, line 54. Use of uninitialized value in numeric gt (>) at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/HSP.pm line 185, line 54. Use of uninitialized value in numeric gt (>) at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/HSP.pm line 197, line 54. -------------------- WARNING --------------------- MSG: Possible error (2) while parsing BLAST report! --------------------------------------------------- Use of uninitialized value in substitution (s///) at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Iteration.pm line 207, line 54. Use of uninitialized value in substitution (s///) at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Iteration.pm line 208, line 54. Use of uninitialized value in substitution (s///) at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Iteration.pm line 209, line 54. Use of uninitialized value in pattern match (m//) at /usr/opt/perl5/lib/site_perl/5.6.0/Bio/Tools/BPlite/Iteration.pm line 211, line 54. I don't know why it doesn't work... I looked at the bioperl API and there is a method "nextSbjct()" for Bio::Tools::BPlite::Iteration ! This is the part of the code: my $seqsfich = Bio::SeqIO->new(-file=>"$proteasa" , '-format' => 'Fasta'); # blast parameters my @pars = ( 'database' => "nr" , 'j' => '2' ); my $factory = Bio::Tools::Run::StandAloneBlast->new(@pars); while (my $seq = $seqsfich->next_seq()) { my $report = $factory->blastpgp($seq); my $max_iter = $report->number_of_iterations; my $iter = $report->round($max_iter); while (my $sbjct = $iter->nextSbjct()){ while (my $hsp = $sbjct->nextHSP()){ printf("%-70s %s\n", substr($hsp->hit->seqname, 0, 70), $hsp->score); } } } The error must be in this part: while (my $sbjct = $iter->nextSbjct()){ while (my $hsp = $sbjct->nextHSP()){ printf("%-70s %s\n", substr($hsp->hit->seqname, 0, 70), $hsp->score); } } because when I remove it from the code, the errors don't appear. What am I doing wrong? Thank you very much. From adarshramakumar at yahoo.co.uk Sun Jan 16 05:13:28 2005 From: adarshramakumar at yahoo.co.uk (Adarsh Ramakumar) Date: Sun, 16 Jan 2005 10:13:28 +0000 (GMT) Subject: [BiO BB] An interesting Domain occurrence? Message-ID: <20050116101328.63445.qmail@web25009.mail.ukl.yahoo.com> Hello All, Is there any where a list of typical domains that exist only in eukaryotes against which I can screen my prokaryotic proteins. The reason for such a question is; I have come across a few proteins in the genome(I am working with) that have Znf_NFX( Znf_NFX1,PF01422) and it looks more to me like a eukaryotic domain (based on Interpro taxon distribution, and also from Pfam species tree).I have screened a few (selective 40) bacterial genomes & I haven't come across its presence either. How ever just like to mention that Interpro could be wrong as I do know of a protein in one more bacterial genome which has this. So now I am very curious to see and cross validate if more such cases happen to be present. I would appreciate any input in this regard. The cynic in me is curious to know if just the occurrence of 6-7 genes with Znf_NFX domains,means anything much, assuming that this domain is strictly non prokaryotic. Further to make it interesting the closest genome relative sharing 96% at 16s level doesn't have even a single copy of this domain, Am i embarking in to something interesting? One may rise the question if these proteins are even expressed and real(not pseudogenes).The lab experiments are clear that these proteins are expressed. The domain have been checked for alignment and they are good as well. Secondly there are many cases I know off where proteins sharing high level of identity(73%) and also annotated to have similar function but when screened them for domains, they do not always share the domain. Any explanation for this please?( except possible HGT, but still........) Any set rules established on architecture of domains in correlation to their occurrence in proteins? I would highly appreciate any inputs you guys can offer in this direction. Have a great day! My ears are very curious to listen to the experts.Just to mention I screen against SMART,Pfam, Prodom,Tigerfam and InterPro. Kindest regards, Adarsh Ramakumar ___________________________________________________________ ALL-NEW Yahoo! Messenger - all new features - even more fun! http://uk.messenger.yahoo.com From stefanielager at fastmail.ca Mon Jan 17 01:26:01 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 17 Jan 2005 06:26:01 +0000 (UTC) Subject: [BiO BB] An interesting Domain occurrence? In-Reply-To: <20050116101328.63445.qmail@web25009.mail.ukl.yahoo.com> Message-ID: <20050117062601.C926D861A30@mail.interchange.ca> Maybe you also could take a look at the Panther HMM database https://panther.appliedbiosystems.com/ . It's released freely now (can be downloaded also) and they use phylogeny when they construct the families. Panther will also be included in Interpro soon http://www.ebi.ac.uk/interpro/release_notes.html Stefanie > Hello All, > Is there any where a list of typical domains that > exist only in eukaryotes against which I can screen my > prokaryotic proteins. The reason for such a question > is; I have come across a few proteins in the genome(I > am working with) that have Znf_NFX( Znf_NFX1,PF01422) > and it looks more to me like a eukaryotic domain > (based on Interpro taxon distribution, and also from > Pfam species tree).I have screened a few (selective > 40) bacterial genomes & I haven't come across its > presence either. How ever just like to mention that > Interpro could be wrong as I do know of a protein in > one more bacterial genome which has this. So now I am > very curious to see and cross validate if more such > cases happen to be present. I would appreciate any > input in this regard. > > The cynic in me is curious to know if just the > occurrence of 6-7 genes with Znf_NFX domains,means > anything much, assuming that this domain is strictly > non prokaryotic. Further to make it interesting the > closest genome relative sharing 96% at 16s level > doesn't have even a single copy of this domain, Am i > embarking in to something interesting? > > One may rise the question if these proteins are even > expressed and real(not pseudogenes).The lab > experiments are clear that these proteins are > expressed. The domain have been checked for alignment > and they are good as well. > > Secondly there are many cases I know off where > proteins sharing high level of identity(73%) and also > annotated to have similar function but when screened > them for domains, they do not always share the domain. > Any explanation for this please?( except possible HGT, > but still........) > > Any set rules established on architecture of domains > in correlation to their occurrence in proteins? > > I would highly appreciate any inputs you guys can > offer in this direction. Have a great day! > My ears are very curious to listen to the experts.Just > to mention I screen against SMART,Pfam, > Prodom,Tigerfam and InterPro. > > Kindest regards, > > Adarsh Ramakumar > > > > > > ___________________________________________________________ > ALL-NEW Yahoo! Messenger - all new features - even more fun! > http://uk.messenger.yahoo.com > _______________________________________________ Bioinformatics.Org > general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From john_abraham_bio at yahoo.com Mon Jan 17 02:07:25 2005 From: john_abraham_bio at yahoo.com (John Abraham) Date: Sun, 16 Jan 2005 23:07:25 -0800 (PST) Subject: [BiO BB] (no subject) Message-ID: <20050117070725.67464.qmail@web53902.mail.yahoo.com> Hi Are there any good papers or review articles that covers in depth about concepts in bioinformatics . Thanks and Regards john __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From holiver at whatifwhatnext.com Mon Jan 17 07:10:10 2005 From: holiver at whatifwhatnext.com (Howard Oliver) Date: Mon, 17 Jan 2005 07:10:10 -0500 Subject: [BiO BB] An interesting Domain occurrence? In-Reply-To: <20050117062601.C926D861A30@mail.interchange.ca> Message-ID: please remove me - thanks Howard Oliver Partner, What If What Next (TM) 1696 Avenue Road, Suite 1005 Toronto, Ontario, M5M 3Y4 (Phone) 416-638-8582 (Cell) 416-568-5254 (Fax) 416-483-5439 holiver at whatifwhatnext.com; holiver at rogers.blackberry.net http://www.whatifwhatnext.com -----Original Message----- From: bio_bulletin_board-bounces at bioinformatics.org [mailto:bio_bulletin_board-bounces at bioinformatics.org]On Behalf Of Stefanie Lager Sent: Monday, January 17, 2005 1:26 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] An interesting Domain occurrence? Maybe you also could take a look at the Panther HMM database https://panther.appliedbiosystems.com/ . It's released freely now (can be downloaded also) and they use phylogeny when they construct the families. Panther will also be included in Interpro soon http://www.ebi.ac.uk/interpro/release_notes.html Stefanie > Hello All, > Is there any where a list of typical domains that > exist only in eukaryotes against which I can screen my > prokaryotic proteins. The reason for such a question > is; I have come across a few proteins in the genome(I > am working with) that have Znf_NFX( Znf_NFX1,PF01422) > and it looks more to me like a eukaryotic domain > (based on Interpro taxon distribution, and also from > Pfam species tree).I have screened a few (selective > 40) bacterial genomes & I haven't come across its > presence either. How ever just like to mention that > Interpro could be wrong as I do know of a protein in > one more bacterial genome which has this. So now I am > very curious to see and cross validate if more such > cases happen to be present. I would appreciate any > input in this regard. > > The cynic in me is curious to know if just the > occurrence of 6-7 genes with Znf_NFX domains,means > anything much, assuming that this domain is strictly > non prokaryotic. Further to make it interesting the > closest genome relative sharing 96% at 16s level > doesn't have even a single copy of this domain, Am i > embarking in to something interesting? > > One may rise the question if these proteins are even > expressed and real(not pseudogenes).The lab > experiments are clear that these proteins are > expressed. The domain have been checked for alignment > and they are good as well. > > Secondly there are many cases I know off where > proteins sharing high level of identity(73%) and also > annotated to have similar function but when screened > them for domains, they do not always share the domain. > Any explanation for this please?( except possible HGT, > but still........) > > Any set rules established on architecture of domains > in correlation to their occurrence in proteins? > > I would highly appreciate any inputs you guys can > offer in this direction. Have a great day! > My ears are very curious to listen to the experts.Just > to mention I screen against SMART,Pfam, > Prodom,Tigerfam and InterPro. > > Kindest regards, > > Adarsh Ramakumar > > > > > > ___________________________________________________________ > ALL-NEW Yahoo! Messenger - all new features - even more fun! > http://uk.messenger.yahoo.com > _______________________________________________ Bioinformatics.Org > general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From karsten.suhre at igs.cnrs-mrs.fr Tue Jan 11 03:33:21 2005 From: karsten.suhre at igs.cnrs-mrs.fr (Karsten Suhre) Date: Tue, 11 Jan 2005 09:33:21 +0100 Subject: [BiO BB] Re: pdb-l: All-vs-All Global protein seq alignment score In-Reply-To: <200501101947.j0AJlMR27795@postal.sdsc.edu> References: <200501101947.j0AJlMR27795@postal.sdsc.edu> Message-ID: <200501110933.21791.karsten.suhre@igs.cnrs-mrs.fr> Hi Manisha, I am not sure what your problem is exactly, but computing pairwise global alignments of distantly related proteins makes little sense. In that case I would rather - for each pair - add a number (5-10) closer homologues for each protein (50-70% homology) and compute a multiple alignment for that set. Here T-Coffee would be my program of choice (it computes multiple alignment scores). On the other hand, if all of your 400 sequences are close homologues, I would use MUSCLE to align all 400 in one go. I would then use protdist from phylip to compute phylogenetic distances between all pairs if that is of use for your purpose. Good luck, Karsten. On Monday 10 January 2005 20:47, Goel, Manisha wrote: > Hi All, > > I have a database of about 400 squences, which I want to compare > All-vs-All to get the global alignment score of each protein sequence > pair. > I tried using bl2seq but that gives me local alignments. > What other program would suit this function best ? > I would probably like to have the flexibility of being able to use > various matrices. > > Thanks a lot, > -Manisha From kingdom at wsu.edu Wed Jan 12 16:06:41 2005 From: kingdom at wsu.edu (Matthew King) Date: Wed, 12 Jan 2005 13:06:41 -0800 Subject: [BiO BB] MrBayes issues in parallel Message-ID: I have implemented parallel MrBayes on our G5 Xserve cluster using MPICH with the Bioteam's Inquiry software. we have 12 dual processor g5's I am having the following issues 1. when I use the nolocal argument with mpirun MrBayes will run through the analyses twice. If I do not use the nolocal argument it runs through only once. i use the command :mpirun -np 4 -nolocal -machinefile /machinefile.freebsd.ppc /mb_mpi datafile.nex I have it set up so that I am using specific machine files to designate which processors to run on. we run only 4 chains so i am only picking 4 processors. I have not yet implemented it into the SGE yet. 2. When I include the quit command at the end of the MrBayes block I get a debugging error WARNING: Memory (2) has not been freed hit any key. This error makes it so the program does not quit automatically. Any ideas would be much appreciated. Matt From virajj at lycos.com Mon Jan 17 12:34:31 2005 From: virajj at lycos.com (vijaya raj) Date: Mon, 17 Jan 2005 12:34:31 -0500 Subject: [BiO BB]classical-papers-in-bioinfo Message-ID: <20050117173432.286B5C610F@ws7-5.us4.outblaze.com> hi john have a look at this site...its a treasure of bioinformatics concepts...starts from blast concept... http://www3.oup.co.uk/jnls/list/nar/special/1/default.html goodluck vijayaraj nagarajan ----- Original Message ----- From: "John Abraham" To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] (no subject) Date: Sun, 16 Jan 2005 23:07:25 -0800 (PST) > > Hi > Are there any good papers or review articles that covers in depth > about concepts in bioinformatics . > > Thanks and Regards > john > > __________________________________________________ > 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 -- _______________________________________________ Find what you are looking for with the Lycos Yellow Pages http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.asp?SRC=lycos10 From beizhuchun at gmail.com Tue Jan 18 04:54:07 2005 From: beizhuchun at gmail.com (Zhu-Chun Bei) Date: Tue, 18 Jan 2005 17:54:07 +0800 Subject: [BiO BB] (no subject) In-Reply-To: <20050117070725.67464.qmail@web53902.mail.yahoo.com> References: <20050117070725.67464.qmail@web53902.mail.yahoo.com> Message-ID: Deer John The following papers may be helpful 1.What is Bioinformatics? A Proposed Definition and Overview of the Field Method Inform Med 2001; 40: 346?58 N. M. Luscombe, D. Greenbaum, M. Gerstein Department of Molecular Biophysics and Biochemistry Yale University, New Haven, USA 2.Molecular Biology Viewed from a Computer Science Perspective. Jacques Cohen Brandeis University Waltham, MA 02254 Jan 23, 1999 Donald Knuth in an interview given on Dec. 1993 at the Computer Literacy Bookshops (http://www.clbooks.com) 3.Bioinformatics in proteomics Mauno Vihinen a,b,* a Institute of Medical Technology, Uniersity of Tampere, FIN- 33014, Tampere, Finland b Tampere Uniersity Hospital, FIN- 33520, Tampere, Finland Biomolecular Engineering 18 (2001) 241?248 4.Early bioinformatics: the birth of a discipline? a personal view Christos A. Ouzounis1,? and Alfonso Valencia2 1Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK, 2Protein Design Group, National Center for Biotechnology, CNB-CSIC Campus U. Autonoma Cantoblanco, Madrid 28049, Spain Bioinformatics Vol. 19 no. 17 2003, pages 2176?2190 On Sun, 16 Jan 2005 23:07:25 -0800 (PST), John Abraham wrote: > Hi > Are there any good papers or review articles that covers in depth about > concepts in bioinformatics . > > Thanks and Regards > john > > __________________________________________________ > 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 > > > -- Zhu-Chun Bei From idoerg at burnham.org Tue Jan 18 18:16:13 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 18 Jan 2005 15:16:13 -0800 Subject: [BiO BB] Announcement: the First Automated Function Prediction Meeting Message-ID: <41ED98BD.10600@burnham.org> Hi all, Please read and forward if you can :) 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) 713 9930 http://ffas.ljcrf.edu/~iddo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: AFP-SIG-announcement.txt URL: From penghanchuan at yahoo.com Tue Jan 18 19:29:19 2005 From: penghanchuan at yahoo.com (Hanchuan Peng) Date: Tue, 18 Jan 2005 16:29:19 -0800 (PST) Subject: [BiO BB] Call for Tutorials for CSB 2005: 4th IEEE Computational Systems Bioinformatics Conference Message-ID: <20050119002919.84634.qmail@web41504.mail.yahoo.com> (We apologize if you receive duplicated copies of this email.) Call for Tutorials CSB 2005: 4th IEEE Computational Systems Bioinformatics Conference The tutorials with be offered on August 8, 2005 at Stanford, CA. Abstracts for tutorials are due February 15, 2005. Tutorial sessions are 2.5 hours either in the morning or the afternoon of August 8th. We invite submissions for tutorials relevant to biomedical informatics. Due to the diverse backgrounds of tutorial attendees, topics spanning biomedicine, computer science and biomedical informatics are appropriate. Appropriate topics include but are not limited to: * Biomedical Visualization and Imaging * Controlled Vocabularies and Ontologies * Biomolecular Analysis, Structure and Function Prediction * Biomolecular modeling including cellular, organ/tissue simulations * Sequence Analysis * Visualization and Analysis of biological networks and pathways * Comparative Genomics * Clinical Systems for Decision Support * Electronic medical records * Microarray technologies for functional genomics * Topics of current biological interest including RNAi, FRET, alternative splicing, gene therapy, etc. * Mass spectrometry and Proteomics * Structural Genomics * Computer security for Patient Privacy Tutorial Proposal Proposals should contain the following information: * Tutorial title. Expected goals and objectives * Detailed outline of the presentation * Intended audience: indicate level with respect to biomedicine, algorithmics, statistics, programming, etc. * Cite relevant qualifications and teaching experience Selection Process All submissions will be evaluated by a committee, which will consider the following criteria in the selection process: * Relevance, interest, and value of the topic to attendees * Expertise and experience of the presenters in the proposed topic * Presentation quality Tutorial Handouts The tutors agree to provide participants with access to materials including: * A detailed outline of the presentation * Copies of the slides * Copies of Supplementary Information General Information Questions about tutorials should be addressed to the tutorial Chair, Betty Cheng at bcheng at stanford.edu or 650-723-2380, and co-chair, Hanchuan Peng at hpeng at lbl.gov, or 510-486-6976. Check http://www.csbcon.org for other information of the conference. __________________________________ Do you Yahoo!? Yahoo! Mail - Easier than ever with enhanced search. Learn more. http://info.mail.yahoo.com/mail_250 From sookjc at yahoo.com Wed Jan 19 15:54:45 2005 From: sookjc at yahoo.com (Sook Jung) Date: Wed, 19 Jan 2005 12:54:45 -0800 (PST) Subject: [BiO BB] ID converter Message-ID: <20050119205445.36956.qmail@web51004.mail.yahoo.com> Hello, Are there any ID converter that can convert the Genbank Acc to AGI(arabidopsis genome initiative) name (eg. AT5G63390) in batch or just a file that lists both of those IDs for all the arabidopsis genes? Thanks, __________________________________ Do you Yahoo!? The all-new My Yahoo! - Get yours free! http://my.yahoo.com From asczyrba at techfak.uni-bielefeld.de Thu Jan 20 03:44:47 2005 From: asczyrba at techfak.uni-bielefeld.de (Alexander Sczyrba) Date: Thu, 20 Jan 2005 09:44:47 +0100 Subject: [BiO BB] d2_cluster output format Message-ID: <41EF6F7F.2040301@techfak.uni-bielefeld.de> Dear Renyi, I found your posting on bioinformatics.org regarding the output format of d2_cluster. Did you get any answers? Do you know the format now? If so, could you send me a description? Thanks! Alex -- ------------------------------------------------------------------------ Alexander Sczyrba Office: M3-111 Technische Fakult?t AG Praktische Informatik Universit?t Bielefeld Tel: +49 521 106 2910 D-33594 Bielefeld Fax: +49 521 106 6411 Germany asczyrba at techfak.uni-bielefeld.de ------------------------------------------------------------------------ From nicolas.goffard at pmtg.u-bordeaux2.fr Thu Jan 20 10:03:35 2005 From: nicolas.goffard at pmtg.u-bordeaux2.fr (Nicolas Goffard) Date: Thu, 20 Jan 2005 16:03:35 +0100 Subject: [BiO BB] ID converter In-Reply-To: <20050119205445.36956.qmail@web51004.mail.yahoo.com> References: <20050119205445.36956.qmail@web51004.mail.yahoo.com> Message-ID: <41EFC847.8060503@pmtg.u-bordeaux2.fr> Se have developed a tool named AliasServer : http://cbi.labri.fr/outils/alias/ for this kind of conversion. Nicolas Sook Jung wrote: > Hello, > > Are there any ID converter that can convert the > Genbank Acc to AGI(arabidopsis genome initiative) name > (eg. AT5G63390) in batch or just a file that lists > both of those IDs for all the arabidopsis genes? > > Thanks, > > > > __________________________________ > Do you Yahoo!? > The all-new My Yahoo! - Get yours free! > http://my.yahoo.com > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- --------------------------------------------------------------- Nicolas Goffard, PhD in Bioinformatics Assistant Lecturer & Researcher Bordeaux BioInformatics Center (CBiB) Universite Victor Segalen Bordeaux 2 146, rue L?o Saignat - 33076 Bordeaux cedex, FRANCE Work: +33 5 57 57 45 71 Mobile: +33 6 11 04 48 62 Fax: +33 5 57 57 16 84 WWW: http://cbi.labri.fr/ WWW: http://nicolas.goffard.free.fr Email: nicolas.goffard at pmtg.u-bordeaux2.fr --------------------------------------------------------------- From sjung at CLEMSON.EDU Fri Jan 21 14:30:35 2005 From: sjung at CLEMSON.EDU (Sook Jung) Date: Fri, 21 Jan 2005 14:30:35 -0500 (EST) Subject: [BiO BB] Re: ID converter (Alias Server) In-Reply-To: <20050121170009.1D095D1F29@www.bioinformatics.org> References: <20050121170009.1D095D1F29@www.bioinformatics.org> Message-ID: <2808.155.138.25.65.1106335835.squirrel@rhblade2.clemson.edu> Dear Nicolas, Thanks for the reply. Somehow I can't get it to work for me. Could you tell me if there's something that I'm doing incorrectly? For example, I pasted in an arabidopsis genbank acc (AAO22800), selected 'GENBANK_AC' and selected 'GENE NAME'. It just says 'No results!' along with all the organism names. It didn't work when I selected 'GI' or 'All' as the identifier type in result. I made a file with a couple of genbank accesions in the right format (reparated by @, no space no carrage return, etc), but it only gave me the error message starting with lines below. ERROR The requested URL could not be retrieved I'll really appreciate your help. Sook > Se have developed a tool named AliasServer : > http://cbi.labri.fr/outils/alias/ for this kind of conversion. > > Nicolas > > Sook Jung wrote: >> Hello, >> >> Are there any ID converter that can convert the >> Genbank Acc to AGI(arabidopsis genome initiative) name >> (eg. AT5G63390) in batch or just a file that lists >> both of those IDs for all the arabidopsis genes? >> >> Thanks, From idonalds at blueprint.org Mon Jan 24 11:53:21 2005 From: idonalds at blueprint.org (Ian Donaldson) Date: Mon, 24 Jan 2005 11:53:21 -0500 Subject: [BiO BB] Re: ID converter (Alias Server) In-Reply-To: <2808.155.138.25.65.1106335835.squirrel@rhblade2.clemson.edu> Message-ID: Hi Sook Have you looked at this file ftp://ftp.geneontology.org/pub/go/gp2protein/gp2protein.tigr_ath Thats what we use for our dbxref module for Arabidopsis. Ian www.blueprint.org/seqhound -----Original Message----- From: bio_bulletin_board-bounces+ian.donaldson=blueprint.org at bioinformatics.or g [mailto:bio_bulletin_board-bounces+ian.donaldson=blueprint.org at bioinform atics.org]On Behalf Of Sook Jung Sent: January 21, 2005 2:31 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Re: ID converter (Alias Server) Dear Nicolas, Thanks for the reply. Somehow I can't get it to work for me. Could you tell me if there's something that I'm doing incorrectly? For example, I pasted in an arabidopsis genbank acc (AAO22800), selected 'GENBANK_AC' and selected 'GENE NAME'. It just says 'No results!' along with all the organism names. It didn't work when I selected 'GI' or 'All' as the identifier type in result. I made a file with a couple of genbank accesions in the right format (reparated by @, no space no carrage return, etc), but it only gave me the error message starting with lines below. ERROR The requested URL could not be retrieved I'll really appreciate your help. Sook > Se have developed a tool named AliasServer : > http://cbi.labri.fr/outils/alias/ for this kind of conversion. > > Nicolas > > Sook Jung wrote: >> Hello, >> >> Are there any ID converter that can convert the >> Genbank Acc to AGI(arabidopsis genome initiative) name >> (eg. AT5G63390) in batch or just a file that lists >> both of those IDs for all the arabidopsis genes? >> >> Thanks, _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From andreas.karlsson at ludesi.com Wed Jan 26 05:17:03 2005 From: andreas.karlsson at ludesi.com (Andreas Karlsson) Date: Wed, 26 Jan 2005 11:17:03 +0100 Subject: [BiO BB] Ludesi 2D Interpreter - 2D gel statistical tool, free for academics Message-ID: <20050126101815.CACA065C4F3@mail1.citynetwork.se> Into Proteomics? Do you run 2D gels? If yes, then you should try Ludesi 2D Interpreter! It's free for academic users! Signup for an account at: www.ludesi.com Ludesi 2D Interpreter is an online tool for statistical evaluation of 2D gel data, accessible from anywhere using only your regular web browser! It can import data from virtually any 2D gel software and gives you an easy to use interface with powerful statistical methods such as Anova, Mann-Whitney, Hierarchical Clustering and Support Vector Machines. Find out what 200 registered users from 22 countries have in common, signup now! www.ludesi.com /The Ludesi 2D Interpreter Team support at ludesi.com Ludesi 2D Interpreter is developed by Ludesi AB, Lund, Sweden. From peng.zhao at plymouth.ac.uk Wed Jan 26 06:25:34 2005 From: peng.zhao at plymouth.ac.uk (Peng Zhao) Date: Wed, 26 Jan 2005 11:25:34 -0000 Subject: [BiO BB] Is there any data for brain disease, for example: Alzheimer's Message-ID: <52A8091888A23F47A013223014B6E9FE01557A79@03-CSEXCH.uopnet.plymouth.ac.uk> Hello, everyone, Do you know if there is any public data available for analysis in brain disease - Alzheimer's? Thanks a lot. Peng From peng.zhao at plymouth.ac.uk Wed Jan 26 06:30:33 2005 From: peng.zhao at plymouth.ac.uk (Peng Zhao) Date: Wed, 26 Jan 2005 11:30:33 -0000 Subject: [BiO BB] Hello Message-ID: <52A8091888A23F47A013223014B6E9FE01557A7A@03-CSEXCH.uopnet.plymouth.ac.uk> Hello, Is there any biodata public available to analyse for Alzheimer's? Thanks, -------------- next part -------------- An HTML attachment was scrubbed... URL: From nikbakht at ibb.ut.ac.ir Wed Jan 26 14:46:41 2005 From: nikbakht at ibb.ut.ac.ir (Hamid Nikbakht) Date: Wed, 26 Jan 2005 23:16:41 +0330 Subject: [BiO BB] Hello In-Reply-To: <52A8091888A23F47A013223014B6E9FE01557A7A@03-CSEXCH.uopnet.plymouth.ac.uk> References: <52A8091888A23F47A013223014B6E9FE01557A7A@03-CSEXCH.uopnet.plymouth.ac.uk> Message-ID: Dear peng, what data do you mean? please specify.. proteins, genes involved in or mechanisms regarding this diseases. Have a nice time. yours Behnam /* ?Hamid( Behnam )Nikbakht, ?M.Sc of Cell and Molecular Sciences, Bioinformatics Center, University of Tehran, ?Tehran, Iran. ?Tel: +98-21-6111-3322 ?Alt. E-Mail : hamid at ibb.ut.ac.ir */ From Nadia.Bolshakova at cs.tcd.ie Thu Jan 27 09:00:11 2005 From: Nadia.Bolshakova at cs.tcd.ie (Nadia Bolshakova) Date: Thu, 27 Jan 2005 14:00:11 -0000 Subject: [BiO BB] CBMS 2005: Submission deadline is extended to February 7, 2005 Message-ID: <006f01c50478$8499b660$6e26e286@DBNJK90J> The 18th IEEE Symposium on Computer-Based Medical Systems SPECIAL TRACK "Bioinformatics and its Medical Applications" http://www.cs.tcd.ie/Nadia.Bolshakova/CBMS_Bioinformatics.html Submission deadline is extended to February 7, 2005 CALL FOR PAPERS Major computational challenges have been raised in the post-genomic era. Novel computational methods and approaches are required to acquire, store, organize, archive, analyse and visualize the large amount of biological and biomedical data. The goal of the track is to share ideas related to bioinformatics challenge among biological, biomedical and computer scientists. Authors are invited to submit original papers addressing any computational biology issue. Papers are invited (but not limited) to the following key themes: Biomedical Research Evolution and Phylogenetics Data Mining in Bioinformatics Microarray Analysis RNAi Analysis Sequence Alignment Pathways, Networks, Systems Biology Functional Genomics Visualization Protein Structure and Analysis Comparative Genomics Pattern Recognition Software Systems IMPORTANT DATES February 7, 2005 - Submission of (6-page, maximum) paper March 1, 2005 - Notification of acceptance March 24, 2005 - Final camera-ready paper due March 24, 2005 - Pre-registration deadline You must pre-register to have your paper published in the proceedings. If you only plan to attend and are not submitting a paper, pre-registration is still strongly encouraged. This conference is space-limited, and registration may not be available on-site. SUBMISSION PROCEDURES FOR PAPER No hardcopy submissions are being accepted; Electronic submissions of original technical research papers will only be accepted in PDF format. File size is limited to 2 MB; Use a maximum of six A4 pages, including figures and references; Include one additional cover sheet, stating the paper title, authors, technical area(s) covered in the article, corresponding author's information (telephone, fax, mailing address, e-mail address), and your preference for oral or poster presentation; Author names should appear only on the cover sheet, not on the summary; Submission in the IEEE Computer Science Press 6x9-inch format is encouraged; Formatting instructions, LaTeX macros and MSWord templates are available at ftp://pubftp.computer.org/press/outgoing/proceedings Authors should indicate the special track title (Bioinformatics and its Medical Applications) on the cover sheet; All submissions should be done electronically via the IEEE CBMS 2005 web submission system at: http://www.cs.tcd.ie/research_groups/mlg/CBMS2005/openconf For further questions, please contact Nadia.Bolshakova at cs.tcd.ie -------------- next part -------------- An HTML attachment was scrubbed... URL: From peng.zhao at plymouth.ac.uk Thu Jan 27 09:18:54 2005 From: peng.zhao at plymouth.ac.uk (Peng Zhao) Date: Thu, 27 Jan 2005 14:18:54 -0000 Subject: [BiO BB] Hello Message-ID: <52A8091888A23F47A013223014B6E9FE01557A80@03-CSEXCH.uopnet.plymouth.ac.uk> Dear Behnam, Thanks for your email. Genes will do. Many Thanks, Peng -----Original Message----- From: bio_bulletin_board-bounces+peng.zhao=plymouth.ac.uk at bioinformatics.org [mailto:bio_bulletin_board-bounces+peng.zhao=plymouth.ac.uk at bioinformatics.org] On Behalf Of Hamid Nikbakht Sent: 26 January 2005 19:47 To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Hello Dear peng, what data do you mean? please specify.. proteins, genes involved in or mechanisms regarding this diseases. Have a nice time. yours Behnam /* ?Hamid( Behnam )Nikbakht, ?M.Sc of Cell and Molecular Sciences, Bioinformatics Center, University of Tehran, ?Tehran, Iran. ?Tel: +98-21-6111-3322 ?Alt. E-Mail : hamid at ibb.ut.ac.ir */ _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From nikbakht at ibb.ut.ac.ir Thu Jan 27 16:09:35 2005 From: nikbakht at ibb.ut.ac.ir (Hamid Nikbakht) Date: Fri, 28 Jan 2005 00:39:35 +0330 Subject: [BiO BB] Hello In-Reply-To: <52A8091888A23F47A013223014B6E9FE01557A80@03-CSEXCH.uopnet.plymouth.ac.uk> References: <52A8091888A23F47A013223014B6E9FE01557A80@03-CSEXCH.uopnet.plymouth.ac.uk> Message-ID: Dear peng, see: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104300 and http://www.ncbi.nlm.nih.gov/Omim/getmap.cgi?l104300 and (focus on 10q24) http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&CHR=10&maps=loc- r,morbid,gene&R1=on&query=AD6&VERBOSE=ON&ZOOM=3 hope to be useful Behnam /* ?Hamid( Behnam )Nikbakht, ?M.Sc of Cell and Molecular Sciences, University of Tehran, Bioinformatics Center, ?Tehran, Iran. ?Tel: +98-21-6111-3322 ?Alt. E-Mail : hamid at ibb.ut.ac.ir */ From peng.zhao at plymouth.ac.uk Thu Jan 27 16:24:37 2005 From: peng.zhao at plymouth.ac.uk (Peng Zhao) Date: Thu, 27 Jan 2005 21:24:37 -0000 Subject: [BiO BB] Hello Message-ID: <52A8091888A23F47A013223014B6E9FE01557A8E@03-CSEXCH.uopnet.plymouth.ac.uk> Dear Behnam, Thanks a lot. I will have a look. Peng -----Original Message----- From: bio_bulletin_board-bounces+peng.zhao=plymouth.ac.uk at bioinformatics.org [mailto:bio_bulletin_board-bounces+peng.zhao=plymouth.ac.uk at bioinformatics.org] On Behalf Of Hamid Nikbakht Sent: 27 January 2005 21:10 To: The general forum at Bioinformatics.Org Subject: RE: [BiO BB] Hello Dear peng, see: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104300 and http://www.ncbi.nlm.nih.gov/Omim/getmap.cgi?l104300 and (focus on 10q24) http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&CHR=10&maps=loc- r,morbid,gene&R1=on&query=AD6&VERBOSE=ON&ZOOM=3 hope to be useful Behnam /* ?Hamid( Behnam )Nikbakht, ?M.Sc of Cell and Molecular Sciences, University of Tehran, Bioinformatics Center, ?Tehran, Iran. ?Tel: +98-21-6111-3322 ?Alt. E-Mail : hamid at ibb.ut.ac.ir */ _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From nikbakht at ibb.ut.ac.ir Fri Jan 28 04:11:33 2005 From: nikbakht at ibb.ut.ac.ir (Hamid Nikbakht) Date: Fri, 28 Jan 2005 12:41:33 +0330 Subject: [BiO BB] Hello (A bour BIO BB) In-Reply-To: <52A8091888A23F47A013223014B6E9FE01557A8E@03-CSEXCH.uopnet.plymouth.ac.uk> References: <52A8091888A23F47A013223014B6E9FE01557A8E@03-CSEXCH.uopnet.plymouth.ac.uk> Message-ID: Dear Peng, Bultin boards are some useful opportunities to let us know about what others know and vice versa, so please use this bultin board system for your non private emails and share with others what you know. I hope you can use this opportunity as well. I myself have learnt and learn many things using this board. Thanks, Behnam /* ?Hamid( Behnam )Nikbakht, ?M.Sc of Cell and Molecular Sciences, Bioiformatics Center, University of Tehran, ?Tehran, Iran. ?Tel: +98-21-6111-3322 ?Alt. E-Mail : hamid at ibb.ut.ac.ir */ From snr_bioinfo at rediffmail.com Sat Jan 29 04:53:29 2005 From: snr_bioinfo at rediffmail.com (Surya Narayana) Date: 29 Jan 2005 09:53:29 -0000 Subject: [BiO BB] Request Message-ID: <20050129095329.11142.qmail@webmail17.rediffmail.com> ? Respected sir i am pursuing my Msc in Bioinformatics in Orissa University of agriculture and Technology .Sir i am going to do my project in mathematical modeling of gene expression controlling factors.So I am looking for some papers on that topic. It would be a great help to me,if somebody can provide me some papers/links or some suggestions, on the mathematical models of these factors in controlling gene expression. Yours obedient Surya Narayana Rath. -------------- next part -------------- An HTML attachment was scrubbed... URL: