From golharam at umdnj.edu Thu Feb 1 12:24:49 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 01 Feb 2007 12:24:49 -0500 Subject: [BiO BB] fastacmd - sequence retreival using "string" ? In-Reply-To: Message-ID: <0613869FD59E483799F731753C3335D9@PICO> If you have the FASTA files used to generate the database, why not simply grep the FASTA file and parse the header that gets returned to you. This way, you now have the GI and can use fastacmd to return you the sequence for that GI. It may not be the cleanest, but is definitely simple enough. Ryan > > > > -----Original Message----- > > From: > > bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform > > atics.org > > [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b > > ioinformatics.org] On Behalf Of Shameer Khadar > > Sent: Wednesday, January 31, 2007 11:46 AM > > To: General Forum at Bioinformatics.Org > > Subject: Fwd: [BiO BB] fastacmd - sequence retreival using > "string" ? > > > > Dear Malcom, > > Thanks for such a detialed reply !!! > > I am sorry for the 'bad description' of my problem. > > > > I am aware that fastacmd -s can search using the Accession ID > > (say a set of > > numbers ), I am looking for an option to quickly search the > > nr database to > > retreive sequence basesd on the "Query String". > > > > For example : If the following is a snippet of a sequence from nr : > > > gi|15674171|ref|NP_268346.1,gi|Homo Sapiens - Kinase 1 > > MTHSTCC..... > > I need to retrieve the above entries (and of course entries > > having similar) > > based on a Query string say "Homo Sapiens". I know this can > > be done using a > > Perl script, and I have coded one for myself, but I need > > something quick > > like fastacmd -s. > > > > Hope you got my question this time. > > Thanks for all the time you spent for me !!! > > -- > > Happy Bioinformatics > > Across the miles... Shameer Khadar > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From jforment at ibmcp.upv.es Fri Feb 2 04:58:43 2007 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Fri, 2 Feb 2007 10:58:43 +0100 Subject: [BiO BB] EST alignment to genome Message-ID: <1170410323.45c30b538b690@webmail.upv.es> Hi,... we need a detailed mapping of every public human EST to the human genome, i.e. which genome position corresponds to each EST nucleotide. I've checked Ensembl an UCSC, but I couldn't find the detailed information there. Any idea? Thank you in advance and best wishes, Javier. -- Javier Forment Millet Instituto de Biologia Molecular y Celular de Plantas (IBMCP) UPV-CSIC Avenida de los Naranjos, s/n 46022 Valencia (SPAIN) jforment at ibmcp.upv.es Tlf.:+34-96-3877885 FAX: +34-96-3877859 From aloraine at gmail.com Fri Feb 2 10:55:25 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 2 Feb 2007 09:55:25 -0600 Subject: [BiO BB] EST alignment to genome In-Reply-To: <1170410323.45c30b538b690@webmail.upv.es> References: <1170410323.45c30b538b690@webmail.upv.es> Message-ID: <83722dde0702020755k48df3ffft8bf5b9e5923cb604@mail.gmail.com> Hello, You can get EST alignments in machine-readable bulk formats from the UCSC Genome Informatics site. Take a look at the the "Tables" link and the "Table Browser" tool. -Ann On 2/2/07, Javier Forment Millet wrote: > Hi,... we need a detailed mapping of every public human EST to the human genome, > i.e. which genome position corresponds to each EST nucleotide. I've checked > Ensembl an UCSC, but I couldn't find the detailed information there. > > Any idea? > > Thank you in advance and best wishes, > > Javier. > > -- > Javier Forment Millet > Instituto de Biologia Molecular y Celular de Plantas (IBMCP) > UPV-CSIC > Avenida de los Naranjos, s/n > 46022 Valencia (SPAIN) > jforment at ibmcp.upv.es > Tlf.:+34-96-3877885 > FAX: +34-96-3877859 > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From barry.hardy at vtxmail.ch Fri Feb 2 07:33:06 2007 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Fri, 02 Feb 2007 13:33:06 +0100 Subject: [BiO BB] Oxford Drug Discovery Workshop, Bursary Award Message-ID: We are holding an eCheminfo Drug Discovery Workshop week at the Chemical Research Laboratory, Oxford University the week of 25-29 June 2007. The approach will be hands-on using an IT classroom and a set of workshops led by application scientists using leading drug discovery software packages. Each workshop will be accompanied by practitioner-led discussions of the methods worked on by the group. Topics to be covered: Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Integration of Cheminformatics & Bioinformatics Tools & Data; Latest advances in ADME & Predictive Toxicology; Pharmacokinetics & Pharmacodynamics and Physiological-based Simulation. More information: Program & Schedule with Abstracts & Bios: http://www.echeminfo.com/COMTY_training/ Program (as pdf): http://barryhardy.blogs.com/cheminfostream/files/eChemProgramOxford07-v3web.PDF News Updates on Cheminfostream Blog: http://barryhardy.blogs.com/cheminfostream/ A Bursary Award sponsored by Chemical Computing Group (CCG) will be used to support the attendance of one academic participant at the Drug Discovery workshop week. You may be working in any area of research related to drug discovery. To apply for the bursary please send an email with a) description of your research; your training needs (ca. 500 words each), b) your CV to echeminfo [-at]- douglasconnect.com by 28 February. The recipient of the award will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on their research progress and will be notified by 15 March. We gratefully acknowledge the sponsorship support of CCG. If interested, please make your reservation early as the size of the group is limited. Contact e-mail Address: echeminfo [-at-] douglasconnect.com best regards Barry Hardy eCheminfo Community of Practice Manager Barry Hardy, PhD Douglas Connect Zeiningen, CH-4314 Switzerland Tel: +41 61 851 0170 From lixue at iastate.edu Fri Feb 2 17:04:45 2007 From: lixue at iastate.edu (Li Xue) Date: Fri, 02 Feb 2007 16:04:45 -0600 Subject: [BiO BB] how to identify the function and structure of a novel sequence Message-ID: <200702022204.l12M4k8p027478@mailhub-3.iastate.edu> hello all, I have a novel sequence(the protein sequence, DNA sequence, the coding sequence, and the cDNA sequence). I tried BLASTn, BLASTx, and PSI-BLAST with default parameters and modified parameters which loosed the restriction to try to find distantly related matches. What I got are only unknown sequences and hypothetical sequences. I also tried EBI Interpro with default parameters. No hits. Can someone offer some ways to identify the function and the structure of a new sequence? Thank you. Li From segura.eduardo at gmail.com Mon Feb 5 03:47:02 2007 From: segura.eduardo at gmail.com (eduardo segura) Date: Mon, 5 Feb 2007 00:47:02 -0800 Subject: [BiO BB] CFP: SPAC 07 - Software Patterns: Addressing Challenges In-Reply-To: References: Message-ID: My apologies for duplicates *The First IEEE International Workshop on **Software Patterns: Addressing Challenges **SPAC 2007 **Call for Papers* *Beijing, China, July 24-27, 2007 (in conjunction with COMPSAC 2007)* * * http://conferences.computer.org/compsac/2007/ (COMPSAC 2007 Link) http://conferences.computer.org/compsac/2007/workshops/SPAC (Workshop Link-1) http://www.engr.sjsu.edu/~fayad/workshops/COMPSAC07 (Workshop Link-2) http://www.vrlsoft.com/workshops/SPAC07 (WorkshopLink-3)* * *THEME OF THE WORKSHOP* As software increases in size and becomes more complex and costly, the need for techniques to ease software development is likewise increasing. Over the last decade, pattern community has evolved and received more interest in both academia and industry. Developing software using patterns holds the promise to reduce the cost and condensing the time of developing software systems, while simultaneously maintaining the quality of these systems. However, the potential of using patterns in developing systems is not fully realized and we need to address many challenges. For example, developing pattern repositories and catalogs, from which patterns can be retrieved and reused, still forms a challenge to software engineering, knowledge engineering and information systems communities. In addition, the need for (semi-) automated approaches for patterns mining and integration poses several open research questions to the software engineering community. Many think these challenges and others preclude the realization of the benefit of patterns as a reuse approach. This workshop aims at bringing together researchers and practitioners who are interested in resolving research challenges or who have practical experience with the different issues of patterns reuse and integration to discuss and advance the state-of-the-art and the state-of-the-practice in patterns reuse. Patterns have emerged as a promising reuse technique for both improving the quality and reducing the cost and time of software development. However, there is an immense belief that patterns have not fulfilled the expectations software developers wanted. Nevertheless, this belief does not rebuff the fact that patterns, as a concept, have the potential to play a key role in developing systems in the near future. This near future will never come unless there are serious attempts from both developers and researchers to investigate and provide creative solutions to current challenges that hinder utilizing patterns in practice. Among these challenges, this workshop focuses on investigating how to develop systems using patterns. We are sure that this topic will attract many developers and researchers in the field to participate in this workshop. *WORKSHOP CHALLENGES* The workshop will address software patterns challenges and debate several issues related to the following questions. We want researchers, framework developers, and application developers to discuss and debate the following questions related to: *I. **Pattern Creation and Development* a. Leaving experience claim on the side, can you show how to create and develop patterns? b. What are the bases of creating patterns? c. Are there guidelines, methodologies, and/or processes for pattern creations and developments? d. Would you show an example or two? *II. **Patterns Selection Process: * a. How does one select analysis and design patterns to build any system? b. What is the basis for selecting these patterns? c. If someone would like to build a system from patterns, how does she select patterns? d. What kind of patterns should one select to build a system from patterns? e. Is there a guideline for the selection process? *III. **Patterns Composition* a. How does one integrate the selected patterns to build any system? or How does one compose any system from patterns? b. What are the various claims related to patterns composition? Are they true? c. Are there guidelines or techniques for patterns composition? Would you illustrate how to use them? *IV. **System of Patterns and General Reuse* a. What do we mean when we say "systems of patterns"? b. Are the various claims related to building any system from patterns reasonable? c. How to develop pattern repositories and catalogs, from which patterns can be retrieved and reused? d. Are there automated approaches for patterns mining and integration? e. What other concepts will help build any system from patterns? . *V. **Impacts* a. What is the impact of software stability on the above issues? Check any of the following websites for all columns and accepted position papers: http://conferences.computer.org/compsac/2007/workshops/SPAC (Main Link) www.engr.sjsu.edu/~fayad//workshops/COMPSAC07 (Workshop Link 2) www.vrlsoft.com/workshops/SPAC07 (Workshop Link 3 -- Under Construction) *PAPER FORMAT AND SUBMISSIONS* Detailed instructions for electronic paper submission and review process can be found at http://www.compsac.org/. People interested in participating in the workshop are requested to submit a short position paper (*3-5 pages*) or regular workshop paper (limited to *6 pages*, double spaced, including figures) representing views and experiences relevant to the discussion topic. The title page should include a maximum 150-word abstract, five keywords, full mailing address, e-mail address, phone number, fax number, and a designated contact author. Papers will be selected depending on the originality, quality and relevance to the workshop. All submitted papers will be evaluated according to its originality, significance, correctness, presentation and relevance. Papers should be submitted electronically at: http://compsac.cs.iastate.edu/2007/SPAC/ . Please follow the instructions given by the web page. Camera Ready manuscripts must be submitted following IEEE conference proceedings style and guidelines. We encourage authors to present novel ideas, critique of existing work, and practical studies. Each accepted paper must be presented in person by the author or one of the authors. To foster lively discussions, each author is encouraged to present open questions and one or two main statements that will be discussed at the workshop. Submissions must be either MS-Word or RTF formats (please, DO NOT compress files). Depending on the number and spread of contributions, the scope may be narrowed to ensure effective communication and information sharing. Accepted position papers will be distributed to the participants before the workshop and made generally available through the WWW and FTP. Accepted papers will be published in the Workshop Proceedings of the 31st IEEE Computer Software and Applications Conference (COMPSAC 2007). At least one of the authors of each accepted paper must register as a full participant in the workshop to have the paper published in the COMPSAC 2007 Proceedings. The workshop selected best papers will be published in online Journal of International Journal Of Patterns (IJOP) ? *www.ijop.org* *WORKSHOP PARTICIPATION* Interested in participating in the workshop without submission are requested to fill out the participation form and e-mail to the co-chair Haitham Hamza , Eduardo Segura , or to the workshop chair M.E. Fayad . ------------------------------------------------- PARTICIPATION FORM: Name and Affiliation: Position: Address: E-mail: URL: Areas of interest: Why would you like to participate? ------------------------------------------------- Please note that registration is required in order to participate in the workshop. An early registration discount is available. An overhead projector and a flipchart will be available. For more information please visit any of the following websites: * * http://conferences.computer.org/compsac/2007/workshops/SPAC (Main Link) www.engr.sjsu.edu/~fayad//workshops/COMPSAC07 (Workshop Link 2) www.vrlsoft.com/workshops/SPAC07 (Workshop Link 3 -- Under Construction) You may also contact the organizers. *PROPOSED AGENDA* 1. Welcome and introduction of participants. The organizers will first give a short overview of any open issues and of the main arguments arising out of the position papers. (Estimated time: 20-30 minutes) 2. Selected authors (representing the main trends) will be given 20 minutes to explain how their position relates to other positions and what each sees as the three major issues. We expect about 5-10 position papers. (Estimated time: 120-130 minutes) 3. The organizers will propose an identification of the major issues, and the participants will then discuss and select what they think are the hottest issues to be examined. (Estimated time: 10-15 minutes) 4. The participants will work for 70-95 minutes in small groups, with a designated moderator in each group. The groups will each deal with two different hot issues identified and will produce a summary in the form of points and counterpoints, showing either how several views are irreducibly opposed or how they are complementary. The number of groups will depend on the number of participants and number of issues selected; ideally there should be 3-5 p people in each group. (Estimated time: 60-70 minutes) 5. Each group will be given 10-15 minutes to present its findings to the workshop. A closing discussion will follow. The workshop report will be written on the basis of these findings and will include an agenda for future exploration and cooperation; it will be made available through the WWW and FTP. (Estimated time: 50-60 minutes for five teams) (Total estimated time: 285-315 minutes, i.e. about five hours +/- 15 minutes; lunch and breaks are not included.) *IMPORTANT DATES* We will be updated based on acceptance process *Feb. 23, 2007*: Full paper and short paper due *Mar. 25, 2007*: Decision notification (electronic) *Apr. 30, 2007*: Camera-ready copy and author registration due *July 24-27, 2007**:* The workshop Date *ORGANIZERS* * * *Chair and Point of Contact:* *Dr.** M.E.** Fayad * Professor of Computer Engineering Computer Engineering Dept., College of Engineering San Jos? State University One Washington Square, San Jos?, CA 95192-0180 Ph: (408) 924-7364, Fax: (408) 924-4153 E-mail: m.fayad at sjsu.edu, me fayad at gmail.com http://www.engr.sjsu.edu/fayad *Co-Chairs:* Dr. H.S. Hamza (Co-Chair) Faculty of Computers and Informatics, Information Technology Department Cairo University, Orman, Giza 12613 - Egypt Ph: (02) 335-8355 (office) E-mail: hshamza at gmail.com * * Eduardo M. Segura vrlSoft, Inc. 2065 Martin Ave., Suite 103 Santa Clara, CA 95050-2707 Phone/Fax: (408) 654-8972 E-mail: esegura at vrlsoft.com, eduardo.segura at sjsu.edu http://www.vrlsoft.com *PROGRAM COMMITTEE* *Leonor Barroca **Open University, England* *Sjaak Brinkkemper Utrecht University, the Netherlands * *Chia-Chu Chiang University of Arkansas at Little Rock, USA* *Rogerio Atem de Carvalho CEFET Campos, Brazil* *Andrea D'Ambrogio University of Roma TorVergata, Italy* *Issam Wajih Damaj Dhofar University, Salalah - Sultanate of Oman * *Khalil DRIRA LAAS-CNRS, France* ** *Islam A. M. El-Maddah Ain Shams University, Egypt* *M.E. Fayad San Jose State University & vrlSoft, Inc., USA* *Joao M. Fernandes Universidade do Minho, Portugal* *IanGraham * *Trireme International Ltd, London, England* *Jiang Guo California State University Los Angeles, USA* *Wilhelm Hasselbring University of Oldenburg, Germany* *Tarek Helmy King Fahd Univ. of Petroleum and Minerals, Saudi Arabia* *H.S. Hamza Cairo University, Egypt* *Pilar Herrero Universidad Polit?cnica de Madrid , Spain.* *Hoda Hosny American University in Cairo, Egypt* *Pao-Ann Hsiung National Chung Cheng University, Chiayi, TAIWAN* *Ali Jaoua University of Qatar, Qatar* *Mohamed-Khireddine KHOLLADI University of Constantine, France* *Dae-Kyoo Kim Oakland University, MI, USA* *Seok-Won Lee The University of North Carolina at Charlotte, USA* *Jeff Lei University of Texas at Arlington, USA* *Ricardo J. Machado Universidade do Minho, Portugal* *Ahmed Mahdy Texas A&M University - Corpus Christi, USA* *Michael Oudshoorn ** Montana State University**, MT, USA* *Srini Ramaswamy University of Arkansas at Little Rock, USA* *Gustavo Rossi LIFIA, Facultad de Informatica, UNLP, Argentina* *Stuart Rubin SPAWAR, SSC-San Diego, USA* *Kannamma Sampath Coimbatore Institute of Technology, India* *Sanchez, Arturo University of North Florida, USA* *Kassem A. Saleh American University of Sharjah, UAE* *Arno Schmidmeier AspectSoft, Hersbruck, Germany * *E.M. Segura San Jose State University & vrlSoft, Inc., USA* *Manolis Tzagarakis Research Academic Technology Institute (RACTI), Greece* *Laurence** T. Yang St Francis Xavier University, Canada* *I-Ling Yen University of Texas at Dallas, USA* From marty.gollery at gmail.com Mon Feb 5 12:12:23 2007 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 5 Feb 2007 09:12:23 -0800 Subject: [BiO BB] how to identify the function and structure of a novelsequence In-Reply-To: <495B86023F645E4AA009D384E5CAD5C13AF7DC@UNRX1.unr.edu> References: <495B86023F645E4AA009D384E5CAD5C13AF7DC@UNRX1.unr.edu> Message-ID: Hi Li, This comes up fairly regularly with new data. Even well studied organisms have many sequences with unknown function. At some point, you just have to get dirty and do a knockout or RNAi knockdown and see what happens to the organism. Marty On 2/5/07, Li Xue wrote: > hello all, > > I have a novel sequence(the protein sequence, DNA sequence, the > coding sequence, and the cDNA sequence). > > I tried BLASTn, BLASTx, and PSI-BLAST with default parameters and > modified parameters which loosed the restriction to try to find > distantly related matches. What I got are only unknown sequences and > hypothetical sequences. > > I also tried EBI Interpro with default parameters. No hits. > > Can someone offer some ways to identify the function and the > structure of a new sequence? Thank you. > > Li > > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS334 775-784-7042 ----------- From karel at javeriana.edu.co Mon Feb 5 13:10:37 2007 From: karel at javeriana.edu.co (Carlos Manuel Estevez-Breton) Date: Mon, 05 Feb 2007 13:10:37 -0500 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 28, Issue 4 In-Reply-To: <20070205170500.C6B2F3696A0@primary.bioinformatics.org> References: <20070205170500.C6B2F3696A0@primary.bioinformatics.org> Message-ID: <45C7731D.5050704@javeriana.edu.co> bio_bulletin_board-request at bioinformatics.org escribi?: > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org > > You can reach the person managing the list at > bio_bulletin_board-owner at bioinformatics.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of BiO_Bulletin_Board digest..." > > > Today's Topics: > > 1. how to identify the function and structure of a novel > sequence (Li Xue) > 2. CFP: SPAC 07 - Software Patterns: Addressing Challenges > (eduardo segura) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 02 Feb 2007 16:04:45 -0600 > From: Li Xue > Subject: [BiO BB] how to identify the function and structure of a > novel sequence > To: bio_bulletin_board at bioinformatics.org > Message-ID: <200702022204.l12M4k8p027478 at mailhub-3.iastate.edu> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > hello all, > > I have a novel sequence(the protein sequence, DNA sequence, the > coding sequence, and the cDNA sequence). > > I tried BLASTn, BLASTx, and PSI-BLAST with default parameters and > modified parameters which loosed the restriction to try to find > distantly related matches. What I got are only unknown sequences and > hypothetical sequences. > > I also tried EBI Interpro with default parameters. No hits. > > Can someone offer some ways to identify the function and the > structure of a new sequence? Thank you. > > Li > Li, Have you tried with structural motifs, bolcks or domains. The method thad we use is search well known structures, mach them and then simulate the no well residues. -- _____________________________________ Carlos Manuel Estevez-Breton R. MSc. Coordinador Unidad de Sistemas Facultad de Ciencias Pontificia Universidad Javeriana Tel (+571) 320 8320 Ext. 4033/32 Av7 No. 40-62 Bogota D.C. Colombia ___________________________________ AVISO LEGAL: El presente correo electronico no representa la opinion o el consentimiento oficial de la PONTIFICIA UNIVERSIDAD JAVERIANA. Este mensaje es confidencial y puede contener informacion privilegiada la cual no puede ser usada ni divulgada a personas distintas de su destinatario. Esta prohibida la retencion, grabacion, utilizacion, aprovechamiento o divulgacion con cualquier proposito. Si por error recibe este mensaje, por favor destruya su contenido y avise a su remitente. En este aviso legal se omiten intencionalmente las tildes. Este mensaje ha sido revisado por un sistema antivirus, por lo que su contenido esta libre de virus. This e-mail has been scanned by an antivirus system, so its contents is free of viruses. From yqzhou at buffalo.edu Mon Feb 5 11:46:06 2007 From: yqzhou at buffalo.edu (Yaoqi Zhou) Date: Mon, 5 Feb 2007 11:46:06 -0500 Subject: [BiO BB] how to identify the function and structure of a novel sequence In-Reply-To: <200702022204.l12M4k8p027478@mailhub-3.iastate.edu> References: <200702022204.l12M4k8p027478@mailhub-3.iastate.edu> Message-ID: <62204F8C-52B9-4C6E-B592-0CE7E32693F8@buffalo.edu> Run on SP3 servers (on service section), http:// sparks.informatics.iupui.edu/ On Feb 2, 2007, at 5:04 PM, Li Xue wrote: > hello all, > > I have a novel sequence(the protein sequence, DNA sequence, the > coding sequence, and the cDNA sequence). > > I tried BLASTn, BLASTx, and PSI-BLAST with default parameters and > modified parameters which loosed the restriction to try to find > distantly related matches. What I got are only unknown sequences > and hypothetical sequences. > > I also tried EBI Interpro with default parameters. No hits. > > Can someone offer some ways to identify the function and the > structure of a new sequence? Thank you. > > Li > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From ishwarayasam at gmail.com Wed Feb 7 09:06:56 2007 From: ishwarayasam at gmail.com (sindhu sambandam) Date: Wed, 7 Feb 2007 19:36:56 +0530 Subject: [BiO BB] software Message-ID: hi does someone know good open source software to produce pdb structures form chemical structures... sindhu From bioinfosm at gmail.com Wed Feb 7 15:41:14 2007 From: bioinfosm at gmail.com (Samantha Fox) Date: Wed, 7 Feb 2007 15:41:14 -0500 Subject: [BiO BB] PWM search tool Message-ID: <726450810702071241u5108ec75xbb56bd2ce9c9f06a@mail.gmail.com> Hey ! I am looking for a good tool on PWM search in DNA sequences. Patser comes across as a popular one but I am uncertain about the threshold score or p-value to use, to count PWM hits. Any views ! ~S From ybolo001 at student.ucr.edu Wed Feb 7 17:09:32 2007 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Wed, 7 Feb 2007 14:09:32 -0800 Subject: [BiO BB] PWM search tool In-Reply-To: <726450810702071241u5108ec75xbb56bd2ce9c9f06a@mail.gmail.com> References: <726450810702071241u5108ec75xbb56bd2ce9c9f06a@mail.gmail.com> Message-ID: <941fcc750702071409w736cf78fyc56daac45b7b96ea@mail.gmail.com> Try googling, motifscanner, On 2/7/07, Samantha Fox wrote: > > Hey ! > > I am looking for a good tool on PWM search in DNA sequences. Patser comes > across as a popular one but I am uncertain about the threshold score or > p-value to use, to count PWM hits. > > Any views ! > > ~S > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Eugene Bolotin Ph.D. candidate Genetics Genomics and Bioinformatics University of California Riverside ybolo001 at student.ucr.edu Dr. Frances Sladek Lab From golharam at umdnj.edu Wed Feb 7 19:28:39 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 07 Feb 2007 19:28:39 -0500 Subject: [BiO BB] PWM search tool In-Reply-To: <726450810702071241u5108ec75xbb56bd2ce9c9f06a@mail.gmail.com> Message-ID: <9267B54084ED420690A2AB23167420C2@PICO> You could use prophecy/profit from the EMBOSS suite. As for a threshold, try calculating the relative score (Absolute score - Min Score)/(Max Score - Min Score) - 100%, where absolute score is the score given by the matrix, and min score is the smallest possible score from the matrix and max score is the maximum possible score. That should tell you how good the score is for any given alignment from the matrix. Ryan --- Ryan Golhar, PhD Informatics Institute of UMDNJ golharam at umdnj.edu > -----Original Message----- > From: > bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.o > rg > [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinfor > matics.org] On Behalf Of Samantha Fox > Sent: Wednesday, February 07, 2007 3:41 PM > To: General Forum at Bioinformatics.Org > Subject: [BiO BB] PWM search tool > > > Hey ! > > I am looking for a good tool on PWM search in DNA sequences. > Patser comes across as a popular one but I am uncertain about > the threshold score or p-value to use, to count PWM hits. > > Any views ! > > ~S > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From golharam at umdnj.edu Wed Feb 7 22:28:40 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 07 Feb 2007 22:28:40 -0500 Subject: [BiO BB] software In-Reply-To: Message-ID: Openbabel perhaps, but it depends on what you mean by a chemical structure > -----Original Message----- > From: > bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.o > rg > [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinfor > matics.org] On Behalf Of sindhu sambandam > Sent: Wednesday, February 07, 2007 9:07 AM > To: The general forum at Bioinformatics.Org > Subject: [BiO BB] software > > > hi > does someone know good open source software to produce pdb > structures form chemical structures... sindhu > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From landman at scalableinformatics.com Wed Feb 7 22:33:24 2007 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 07 Feb 2007 22:33:24 -0500 Subject: [BiO BB] software In-Reply-To: References: Message-ID: <45CA9A04.9060207@scalableinformatics.com> sindhu sambandam wrote: > hi > does someone know good open source software to produce pdb structures form > chemical structures... Do you mean primary protein sequence data from 3D structures, or 3D structures from primary sequence data? Or do you mean something else entirely? -- 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 or +1 866 888 3112 cell : +1 734 612 4615 From rb at hcl.in Wed Feb 7 23:11:33 2007 From: rb at hcl.in (Balamurugan.R) Date: Thu, 8 Feb 2007 09:41:33 +0530 Subject: [BiO BB] software In-Reply-To: <45CA9A04.9060207@scalableinformatics.com> Message-ID: <200702080404.l1844Atk008964@mispmo.hcl.in> You can try prodrg server if your molecule is small http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Thanks and Best Regards, Balamurugan.R -----Original Message----- From: bio_bulletin_board-bounces+rb=hcl.in at bioinformatics.org [mailto:bio_bulletin_board-bounces+rb=hcl.in at bioinformatics.org] On Behalf Of Joe Landman Sent: Thursday, February 08, 2007 9:03 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] software sindhu sambandam wrote: > hi > does someone know good open source software to produce pdb structures form > chemical structures... Do you mean primary protein sequence data from 3D structures, or 3D structures from primary sequence data? Or do you mean something else entirely? -- 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 or +1 866 888 3112 cell : +1 734 612 4615 _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From golharam at umdnj.edu Thu Feb 8 10:05:01 2007 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 08 Feb 2007 10:05:01 -0500 Subject: [BiO BB] software In-Reply-To: <200702080404.l1844Atk008964@mispmo.hcl.in> Message-ID: <3982E06916A04D9B9B28A9CAD4F36667@PICO> For small molecules, the only open source structure builder I am aware of is ghemical (See http://www.uku.fi/~thassine/projects/ghemical/) > -----Original Message----- > From: > bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.o > rg > [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinfor > matics.org] On Behalf Of Balamurugan.R > Sent: Wednesday, February 07, 2007 11:12 PM > To: 'General Forum at Bioinformatics.Org' > Subject: RE: [BiO BB] software > > > You can try prodrg server if your molecule is small > http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ > > > Thanks and Best Regards, > Balamurugan.R > -----Original Message----- > From: bio_bulletin_board-bounces+rb=hcl.in at bioinformatics.org > [mailto:bio_bulletin_board-bounces+rb=hcl.in at bioinformatics.or g] On Behalf Of Joe Landman Sent: Thursday, February 08, 2007 9:03 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] software sindhu sambandam wrote: > hi > does someone know good open source software to produce pdb structures > form chemical structures... Do you mean primary protein sequence data from 3D structures, or 3D structures from primary sequence data? Or do you mean something else entirely? -- 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 or +1 866 888 3112 cell : +1 734 612 4615 _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From keshet1 at umbc.edu Wed Feb 7 22:39:12 2007 From: keshet1 at umbc.edu (Ben Keshet) Date: Wed, 7 Feb 2007 22:39:12 -0500 Subject: [BiO BB] software In-Reply-To: Message-ID: <000001c74b32$b2ea5c60$29ad5582@umbc80a173302c> Sindhu wrote: > hi > does someone know good open source software to produce pdb > structures form chemical structures... sindhu Hi, If you have the coordinates you can try http://www.proteinscope.com/ (if I understood your question.) BK > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From frcerqueira at gmail.com Mon Feb 12 07:30:21 2007 From: frcerqueira at gmail.com (Fabio Cerqueira) Date: Mon, 12 Feb 2007 13:30:21 +0100 Subject: [BiO BB] Mascot parameters Message-ID: <50fceb2c0702120430u42780a2ch536b9e74f41e4537@mail.gmail.com> Hi, Does anybody there use Mascot for protein identification by MS/MS ion serch? I'm trying to use it for the first time, but I don't know how options to check in the fixed and variable modifications. Concerning the fixed modifications I'd like to indicate a C-term mass of 14.01570; and for the amino acids C, D, E the masses: 160.03068, 129.04264, and 143.05829, respectively. Concerning the variable modifications, I'd like to indicate phosphorylation, oxidation of methionine and loss of water in amino acids S and T. Phosphorylation and oxidation of methionine are easy. But I don't know how option to choose concerning the loss of water in S and T. Could anybody help me? Thanks, Fabio. From marchywka at hotmail.com Mon Feb 12 08:02:31 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 12 Feb 2007 08:02:31 -0500 Subject: [BiO BB] Mascot parameters In-Reply-To: <50fceb2c0702120430u42780a2ch536b9e74f41e4537@mail.gmail.com> Message-ID: Would anyone be willing to post a link to a tutorial or give us a quick explanation of the issues involved in precise protein identification and quantification? I'm interested in a practical problems in immunology where you read about results like this: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16463039&query_hl=3&itool=pubmed_docsum "Immunization with oxidized ovarian tumor cell lines may represent an improved therapeutic strategy to stimulate a polyclonal anti-tumor cellular immune response and hence extend remission in ovarian cancer." and have to ask, " if you wanted to prepare a pure, highly immunogenic antigen, should you make it with clean side chains or should you oxidize or otherwise modify some of them?" If you were a dendritic cell looking for the results of a neutrophil attack, you may suspect that the HOCl or H2O2 modified proteins are good candidates for being from pathogens. Some drugs that seem to produce autoimmune reactions seem to do so by covalently modifiying host proteins- you really have to suspect that small amounts of unusual proteins could be very interesting. If you design a dendritic cell vaccine using a single defined antigen you may reasonably speculate that observed immune response could be due to modified versions ("impurities" ) of the intended antigen. How hard would it be to find out what is actually in your "pure antigen" ? ( presumably you would then attempt to make something which consists primarily of each impurity and test it for immunogenicity) I've always wondered what the limitations are for identifcation and measurement of these things. Thanks. >From: "Fabio Cerqueira" >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: [BiO BB] Mascot parameters >Date: Mon, 12 Feb 2007 13:30:21 +0100 > >Hi, > >Does anybody there use Mascot for protein identification by MS/MS ion >serch? >I'm trying to use it for the first time, but I don't know how options to >check in >the fixed and variable modifications. > >Concerning the fixed modifications I'd like to indicate a C-term mass of >14.01570; and for the amino acids C, D, E the masses: 160.03068, >129.04264, and 143.05829, respectively. > >Concerning the variable modifications, I'd like to indicate >phosphorylation, >oxidation of methionine and loss of water in amino acids S and T. >Phosphorylation and oxidation of methionine are easy. But I don't know >how option to choose concerning the loss of water in S and T. > >Could anybody help me? > >Thanks, Fabio. >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Invite your Hotmail contacts to join your friends list with Windows Live Spaces http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/?href=http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us From ethan.strauss at promega.com Mon Feb 12 09:59:05 2007 From: ethan.strauss at promega.com (Ethan Strauss) Date: Mon, 12 Feb 2007 08:59:05 -0600 Subject: [BiO BB] Learning R Message-ID: Hi, I am interested in learning R. I probably won't be using it a great deal, but it useful to know more about so that I can better understand what it is, how it is used and so forth. Does anyone know of any good books, web sites, online courses, or even short courses, which teach R for bioinformatics? Thanks! Ethan Ethan Strauss Ph.D. Bioinformatics Scientist Promega Corporation 2800 Woods Hollow Rd. Madison, WI 53711 608-274-4330 800-356-9526 ethan.strauss at promega.com From jeff at bioinformatics.org Mon Feb 12 10:22:08 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 12 Feb 2007 10:22:08 -0500 Subject: [BiO BB] Learning R In-Reply-To: References: Message-ID: <45D08620.6060006@bioinformatics.org> Hi Ethan, Bioinformatics.Org has been running "R for Biologists" courses recently. A level 1 course is starting today, and a level 2 course is starting next week: http://edu.bioinformatics.org/AJ http://edu.bioinformatics.org/AH It's likely we'll run these again before the summer. Also, Bioconductor.org lists some of the other R workshops out there: http://bioconductor.org/workshops Cheers, Jeff Ethan Strauss wrote: > I am interested in learning R. I probably won't be using it a > great deal, but it useful to know more about so that I can better > understand what it is, how it is used and so forth. Does anyone know of > any good books, web sites, online courses, or even short courses, which > teach R for bioinformatics? > Thanks! > Ethan -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From onsongo at cs.umn.edu Sun Feb 11 13:17:56 2007 From: onsongo at cs.umn.edu (onsongo at cs.umn.edu) Date: 11 Feb 2007 12:17:56 -0600 Subject: [BiO BB] uniprot (relational database implementation) In-Reply-To: <726450810702071241u5108ec75xbb56bd2ce9c9f06a@mail.gmail.com> References: <726450810702071241u5108ec75xbb56bd2ce9c9f06a@mail.gmail.com> Message-ID: Hello, I was wondering if there is a relational database implementation of uniprot around. thanks, Getiria From marty.gollery at gmail.com Mon Feb 12 10:20:25 2007 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 12 Feb 2007 07:20:25 -0800 Subject: [BiO BB] Learning R In-Reply-To: <495B86023F645E4AA009D384E5CAD5C13AF8C3@UNRX1.unr.edu> References: <495B86023F645E4AA009D384E5CAD5C13AF8C3@UNRX1.unr.edu> Message-ID: Try this one Ethan: Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health) by Robert Gentleman, Vincent Carey, Wolfgang Huber, and Rafael Irizarry Marty On 2/12/07, Ethan Strauss wrote: > Hi, > I am interested in learning R. I probably won't be using it a > great deal, but it useful to know more about so that I can better > understand what it is, how it is used and so forth. Does anyone know of > any good books, web sites, online courses, or even short courses, which > teach R for bioinformatics? > Thanks! > Ethan > > Ethan Strauss Ph.D. > Bioinformatics Scientist > Promega Corporation > 2800 Woods Hollow Rd. > Madison, WI 53711 > 608-274-4330 > 800-356-9526 > ethan.strauss at promega.com > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS334 775-784-7042 ----------- From ethan.strauss at promega.com Mon Feb 12 10:33:04 2007 From: ethan.strauss at promega.com (Ethan Strauss) Date: Mon, 12 Feb 2007 09:33:04 -0600 Subject: [BiO BB] Learning R Message-ID: That's exactly what I was looking for. Thanks! Ethan -----Original Message----- From: bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformat ics.org] On Behalf Of J.W. Bizzaro Sent: Monday, February 12, 2007 9:22 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Learning R Hi Ethan, Bioinformatics.Org has been running "R for Biologists" courses recently. A level 1 course is starting today, and a level 2 course is starting next week: http://edu.bioinformatics.org/AJ http://edu.bioinformatics.org/AH It's likely we'll run these again before the summer. Also, Bioconductor.org lists some of the other R workshops out there: http://bioconductor.org/workshops Cheers, Jeff Ethan Strauss wrote: > I am interested in learning R. I probably won't be using it a great > deal, but it useful to know more about so that I can better understand > what it is, how it is used and so forth. Does anyone know of any good > books, web sites, online courses, or even short courses, which teach R > for bioinformatics? > Thanks! > Ethan -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From aloraine at gmail.com Tue Feb 13 19:19:58 2007 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 13 Feb 2007 18:19:58 -0600 Subject: [BiO BB] plotter and tabular data - visualization Message-ID: <83722dde0702131619q368f656dkf099cbab6cd7478@mail.gmail.com> Hello all, I'm looking for a (kind of) specialized visualization tool, which I'm sure must already exist...hopefully one of you can point me in the right direction. I want something that can read in columns of numbers, where each row might be labeled with some value, such as a microarray slide id, or something like that. Then, I want to plot the columns of numbers against each other (a scatter plot), so that I can, by eye, recognize any interesting patterns relating one column to another, such as a linear relationship, or correlation. There are of course lots of programs that can do the plotting part relatively easily, but I what I want on top of this is the ability to interact with the plot. For example, I want the tool to display the original data in a sort of Excel-style spreadsheet format, so that I can click on one or more rows or cells the spreadsheet and see the corresponding points in the plot "light up." Likewise, I want to be able to click on points in the plot, and see the corresponding rows get highlighted. R has something like this, but it is very clumsy and awkward -- at least, it was clumsy and awkard the last time I tried it, which was a few years ago. Maybe there's something better now? Please let me know if you have used something like this .. or just heard about it! Yours, Ann Loraine -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From christoph.gille at charite.de Wed Feb 14 11:08:34 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 14 Feb 2007 17:08:34 +0100 (CET) Subject: [BiO BB] plotter and tabular data - visualization In-Reply-To: <83722dde0702131619q368f656dkf099cbab6cd7478@mail.gmail.com> References: <83722dde0702131619q368f656dkf099cbab6cd7478@mail.gmail.com> Message-ID: <34077.141.42.56.114.1171469314.squirrel@webmail.charite.de> I like xmgrace because one can set up the graph layout interactively and apply the layout to different data given in plain text file. It can be run in batch mode. From harry.mangalam at uci.edu Wed Feb 14 13:23:29 2007 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Wed, 14 Feb 2007 10:23:29 -0800 Subject: [BiO BB] plotter and tabular data - visualization In-Reply-To: <83722dde0702131619q368f656dkf099cbab6cd7478@mail.gmail.com> References: <83722dde0702131619q368f656dkf099cbab6cd7478@mail.gmail.com> Message-ID: <200702141023.29871.harry.mangalam@uci.edu> What you might be thinking of is ggobi (the gtk son of xgobi). http://www.ggobi.org/ It's now integrated well into R and has the interactive brushing (highlighting and selecting of points), 3d visualization, multi-variate simultaneous visualization, etc. It is NOT all that intuitive to set up for independent use (you have to (or had to) re-format your data into XML - ugh), but it works with R data frames transparently. Plus, in R, it has access to all of R's goodies. If you're going to be doing this more than a one-off, it's a great tool and worth the activation energy. If you want a tool that does just about everything, check out Visit: http://www.llnl.gov/VisIt/home.html and for scripted plotting, it's hard to beat good old gnuplot. It's not particularly interactive, but you can zoom interactively into the plot pane for large data sets. For repetitive plots of large data sets, it's fabulous. Slightly off-topic but only just, you might also want to visit IBM's Many Eyes site: http://services.alphaworks.ibm.com/manyeyes/app and the similarly tilted http://www.swivel.com for innovative ways to approach and visualize data. hjm On Tuesday 13 February 2007 16:19, Ann Loraine wrote: > Hello all, > > I'm looking for a (kind of) specialized visualization tool, which > I'm sure must already exist...hopefully one of you can point me in > the right direction. > > I want something that can read in columns of numbers, where each > row might be labeled with some value, such as a microarray slide > id, or something like that. > > Then, I want to plot the columns of numbers against each other (a > scatter plot), so that I can, by eye, recognize any interesting > patterns relating one column to another, such as a linear > relationship, or correlation. > > There are of course lots of programs that can do the plotting part > relatively easily, but I what I want on top of this is the ability > to interact with the plot. > > For example, I want the tool to display the original data in a sort > of Excel-style spreadsheet format, so that I can click on one or > more rows or cells the spreadsheet and see the corresponding points > in the plot "light up." Likewise, I want to be able to click on > points in the plot, and see the corresponding rows get highlighted. > > R has something like this, but it is very clumsy and awkward -- at > least, it was clumsy and awkard the last time I tried it, which was > a few years ago. Maybe there's something better now? > > Please let me know if you have used something like this .. or just > heard about it! > > Yours, > > Ann Loraine -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824 0084(o), 949 285 4487(c) harry.mangalam at uci.edu From kiran.soorya at gmail.com Wed Feb 14 03:02:19 2007 From: kiran.soorya at gmail.com (soorya kiran) Date: Wed, 14 Feb 2007 13:32:19 +0530 Subject: [BiO BB] Phylogenetic Distance calculation Message-ID: Good day all, Can anyone tell how can I find evolutionary distance (Year) from a given set of amino acid sequences, provided we have constructed the phylogram ? Thanks in advance. Srijith From goletsis at cc.uoi.gr Wed Feb 14 13:24:13 2007 From: goletsis at cc.uoi.gr (yorgos goletsis) Date: Wed, 14 Feb 2007 20:24:13 +0200 Subject: [BiO BB] QA-Gen Workshop. CFP - Deadline April 4, 2007 Message-ID: <45D353CD.4050403@cc.uoi.gr> CALL FOR PAPERS QA-Gen Workshop webpage: http://www.iccs.info/qa_gen.php QA-gen Workshop: Quantitative approaches for knowledge discovery and decision support in the post genomic era In conjunction with the 15th International Conference on Conceptual Structures (ICCS 2007) 22-27 of July, 2007, Sheffield Hallam University, UK Call for Papers and Participation Bioinformatics research is booming and genomics, proteomics or even metabolomics are the words of the moment. It is the sequencing of the human genome that is expected to bring about a major impact on the prevention, diagnosis, treatment, monitoring, and outcome of several diseases. Progress will most likely occur in a stepwise fashion with the biggest initial impact in diagnosis and molecular targeting of new medicines. This abundance of new data, however, requires the combination of statistical and machine learning techniques for the efficient extraction of knowledge and analysis of data. Modelling, simulation, pattern analysis, image analysis and data mining algorithms and techniques that combine good performance both in terms of accuracy and computational efficiency appear as a necessity if we want such systems to be put in practice and to support clinical practice (diagnosis, prognosis, treatment selection, drug design). The goal of this workshop is to explore state-of-art approaches and challenges on the field. Topics Topics to be addressed in the submissions, include (without being limited to) quantitative analysis, knowledge based or artificial intelligence applications in bioinformatics related to: * Expression analysis * Sequence analysis * Structure prediction * Image processing, quantification and analysis * Web services and platforms * Ontology engineering * Simulation tools * In-silico oncology * Algorithms & tools to support knowledge discovery * Models & tools to support clinical bioinformatics Submission Details Both contributions with a theoretical and a practical focus are welcome. Papers could demonstrate algorithms and techniques related to quantitative analysis and knowledge discovery in the bioinformatics domain but also practical application and systems for related decision support. Papers will be reviewed for adherence to the workshop scope and quality by the chairs and additional reviewers. Approximately 10-12 papers will be selected for presentation. Accepted papers of appropriate quality will be published in an ISBN numbered ICCS-2007 Workshop Volume by Springer. Important Dates * Paper submission: o Directly to the workshop chairs via e-mail o Deadline: April 4, 2007. 5-6 pages, in PDF format, following the Springer LNCS rules. See the Workshops web site * Notification of acceptance: April 15, 2007 * Camera ready copy: April 28, 2007 * Workshop: July, 22 and 23 of July 2007. Program Chairs * Yorgos Goletsis, University of Ioannina, Greece, Technical Manager of MATCH project (e-mail: goletsis AT cc DOT uoi DOT gr) * Costas Papaloukas, University of Ioannina, Greece (e-mail: papalouk AT cc DOT uoi DOT gr) Further Information For further information on the workshop you can contact directly the conference chair. See the ICCS 07 website for further information on ICCS 2007. http://www.iccs.info You can contact the workshop organisers directly for any further information. The workshop is organised within the framework of MATCH project (IST-2005-027266) with the co-operation of University of Patras, Sheffield Halam University and University of Ioannina. From logan at cacs.louisiana.edu Wed Feb 14 16:59:03 2007 From: logan at cacs.louisiana.edu (Raja Loganantharaj) Date: Wed, 14 Feb 2007 15:59:03 -0600 Subject: [BiO BB] Looking for interaction plot with weight Message-ID: <45D38627.8010302@cacs.louisiana.edu> Colleagues: I am looking for a graph display program that place nodes with the distance proportional to the distance given in a matrix. The input is a matrix of distances among the nodes. I appreciate your help. I have seen such plots in some bioinformatics publications, but the authors do not reveal which programs they have used. Appreciate your help. From skhadar at gmail.com Thu Feb 15 00:56:28 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 15 Feb 2007 11:26:28 +0530 Subject: [BiO BB] Phylogenetic Distance calculation In-Reply-To: References: Message-ID: Srijith, Can you tell me how you created your Phylogram ? Is it using the standard Phylogeny protocol MSA -> SEQBOOT (Value) -> ProtDist -> Neighbor - Consensus -> Phylogram / Dendrogram ? If that was the case, you will get a picture of evolution based on bootstrap support , but not in terms of year. PS: I am sorry that your question is not clear to me (may be I didnt get what you are looking for :| ). Cheers, Shameer NCBS - TIFR On 2/14/07, soorya kiran wrote: > > Good day all, > > Can anyone tell how can I find evolutionary distance (Year) from a given > set > of amino acid sequences, provided we have constructed the phylogram ? > > > Thanks in advance. > > Srijith > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From skhadar at gmail.com Thu Feb 15 03:07:00 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 15 Feb 2007 13:37:00 +0530 Subject: [BiO BB] Phylogenetic Distance calculation In-Reply-To: References: Message-ID: Have a look at this article : Baldauf SL: *Phylogeny for the faint of heart: a tutorial.* *Trends Genet* 2003, *19**:*345-351. Cheers, -- Shameer On 2/15/07, Shameer Khadar wrote: > > Srijith, > Can you tell me how you created your Phylogram ? > Is it using the standard Phylogeny protocol MSA -> SEQBOOT (Value) -> > ProtDist -> Neighbor - Consensus -> Phylogram / Dendrogram ? If that was the > case, you will get a picture of evolution based on bootstrap support , but > not in terms of year. > > PS: I am sorry that your question is not clear to me (may be I didnt get > what you are looking for :| ). > > Cheers, > Shameer > NCBS - TIFR > > > On 2/14/07, soorya kiran wrote: > > > > Good day all, > > > > Can anyone tell how can I find evolutionary distance (Year) from a given > > set > > of amino acid sequences, provided we have constructed the phylogram ? > > > > > > Thanks in advance. > > > > Srijith > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > From aloraine at gmail.com Thu Feb 15 03:12:07 2007 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 15 Feb 2007 02:12:07 -0600 Subject: [BiO BB] Looking for interaction plot with weight In-Reply-To: <45D38627.8010302@cacs.louisiana.edu> References: <45D38627.8010302@cacs.louisiana.edu> Message-ID: <83722dde0702150012l500f6eb2y2c9e7c8d94d4bbfe@mail.gmail.com> Hello, You might check out graphexplore: http://graphexplore.cgt.duke.edu/ They provide Java Web Start launch pages and examples. -Ann On 2/14/07, Raja Loganantharaj wrote: > Colleagues: > I am looking for a graph display program that place nodes with the > distance proportional to the distance given in a matrix. The input is a > matrix of distances among the nodes. I appreciate your help. I have > seen such plots in some bioinformatics publications, but the authors do > not reveal which programs they have used. > > Appreciate your help. > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From forward at hongyu.org Wed Feb 14 16:22:27 2007 From: forward at hongyu.org (Hongyu Zhang) Date: Wed, 14 Feb 2007 13:22:27 -0800 (PST) Subject: [BiO BB] SNP analysis program Message-ID: <300253.51793.qm@web51414.mail.yahoo.com> Dear all, I am looking for a SNP analysis program, which is good at Assemble chromats Allow me to edit chromats Displays mixed bases Displays polymorphisms calls We have looked at Polyphred and Sequencher. Polyphred works well in Linux/Unix, so it can be wrapped in a shell script to run in batch mode processing bulk data. It is also in good compatibility with Phred/Phrap and consed. Sequencher has nice GUI and runs on Windows, which is good for scientist to do annotation interactively, but I am not sure whether it can be run in batch mode. If you have any good suggestions, please let me know. Thanks! Hongyu Zhang, Ph.D. Computational biologist Ceres Inc., Thousand Oaks, CA Cell: 805-405-5394 Fax: 866-447-8750 From mourad12345678 at yahoo.com Wed Feb 14 19:43:13 2007 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Wed, 14 Feb 2007 16:43:13 -0800 (PST) Subject: [BiO BB] Call for Papers : ALBIO'07 (Algorithms in Molecular Biology) Message-ID: <895858.94463.qm@web31505.mail.mud.yahoo.com> CALL FOR PAPERS ALBIO'07 Algorithms in Molecular Biology Session of BIOCOMP'07 The 2007 International Conference on Bioinformatics & Computational Biology Monte Carlo Resort, Las Vegas, Nevada, USA (June 25-28, 2007) www.worldacademyofscience.org/worldcomp07/ws/BIOCOMP07 Computational Molecular Biology has emerged from the Human Genome Project as an important discipline for academic research and industrial application. The growing size of biological databases, the complexity of biological problems and the necessity to deal with errors in biological sequences all result in large run time and memory requirements. Biological sequence databases are growing at an exponential rate. All of these factors will make the development of fast, low memory requirements and high-performances algorithms increasingly important in Computational Molecular Biology. In our session, we are interested in papers that deal with all aspects of algorithms in Molecular Biology. We are, particularly, interested in algorithms that address fundamental and/or applied problems in Molecular Biology that are computationally efficient, that have been implemented and experimented on simulated and/or on real biological sequences and that provide interesting new results. The submitted papers should present recent research results and identify and explore directions for future research. Topics include, but not limited to: (i) strings processing, (ii) biological sequences comparison, (iii) structures prediction, (iv) phylogeny reconstruction, (v) DNA sequences assembly, clustering, and mapping, (vi) molecular evolution, (vii) genes prediction/recognition, (viii) genes expression (ix) haplotyping (x) genomes rearrangement. INSTRUCTIONS TO AUTHORS You are invited to submit a draft paper in Word or PDF format, about 5 to 8 pages including figures and references, before March 15, 2007 to the Session Chair : Dr. Mourad Elloumi : E.Mail: Mourad.Elloumi at fsegt.rnu.tn or Mourad12345678 at yahoo.com Important Dates March 15, 2007 : Draft paper (about 5 to 8 pages) submissions due March 31, 2007 : Notification of acceptance April 20, 2007 : Final camera-ready papers & pre-registration due June 25-28, 2007 : BIOCOMP'07 Conference ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From MEC at Stowers-Institute.org Thu Feb 15 13:09:59 2007 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Thu, 15 Feb 2007 12:09:59 -0600 Subject: [BiO BB] SNP analysis program Message-ID: http://bioinformatics.org/pipermail/bio_bulletin_board/2006-May/003215.h tml > -----Original Message----- > From: > bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform > atics.org > [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b > ioinformatics.org] On Behalf Of Hongyu Zhang > Sent: Wednesday, February 14, 2007 3:22 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] SNP analysis program > > Dear all, > > I am looking for a SNP analysis program, which is good at > > Assemble > chromats > Allow me to edit > chromats > > Displays mixed > bases > > Displays polymorphisms > calls > > > > We have looked at Polyphred and Sequencher. Polyphred works well in > Linux/Unix, so it can be wrapped in a shell script to run in > batch mode > processing bulk data. It is also in good compatibility with > Phred/Phrap > and consed. Sequencher has nice GUI and runs on Windows, which is good > for scientist to do annotation interactively, but I am not > sure whether > it can be run in batch mode. > > If you have any good suggestions, please let me know. Thanks! > > > > Hongyu Zhang, Ph.D. > Computational biologist > Ceres Inc., Thousand Oaks, CA > Cell: 805-405-5394 > Fax: 866-447-8750 > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Alex.Bossers at wur.nl Fri Feb 16 03:16:59 2007 From: Alex.Bossers at wur.nl (Bossers, Alex) Date: Fri, 16 Feb 2007 09:16:59 +0100 Subject: [BiO BB] SNP analysis program In-Reply-To: <300253.51793.qm@web51414.mail.yahoo.com> Message-ID: <47C53C762312C548BF23B6556377B3EB5206EC@scomp0038.wurnet.nl> We have been using Mutation Surveyor from Softgenetics for large scale SNP detection (eukaryotic). Although commercial, it works great. For large EST assemblies (depending on the source EST/genomic) we have been using the package from TIGR called TGICL. Good luck, Alex -----Oorspronkelijk bericht----- Van: bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.org [mailto:bio_bulletin_board-bounces+alex.bossers=wur.nl at bioinformatics.or g] Namens Hongyu Zhang Verzonden: woensdag 14 februari 2007 22:22 Aan: bio_bulletin_board at bioinformatics.org Onderwerp: [BiO BB] SNP analysis program Dear all, I am looking for a SNP analysis program, which is good at Assemble chromats Allow me to edit chromats Displays mixed bases Displays polymorphisms calls We have looked at Polyphred and Sequencher. Polyphred works well in Linux/Unix, so it can be wrapped in a shell script to run in batch mode processing bulk data. It is also in good compatibility with Phred/Phrap and consed. Sequencher has nice GUI and runs on Windows, which is good for scientist to do annotation interactively, but I am not sure whether it can be run in batch mode. If you have any good suggestions, please let me know. Thanks! Hongyu Zhang, Ph.D. Computational biologist Ceres Inc., Thousand Oaks, CA Cell: 805-405-5394 Fax: 866-447-8750 _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From kiran.soorya at gmail.com Fri Feb 16 23:46:17 2007 From: kiran.soorya at gmail.com (soorya kiran) Date: Sat, 17 Feb 2007 10:16:17 +0530 Subject: [BiO BB] Phylogenetic Distance calculation In-Reply-To: References: Message-ID: *Hai Shameer,* ** *Thank you for the interest you have shown.* *We took the same path quoted by you with slight changes. As the sequence was DNA we used DnaDist. We used Phylodraw for tree construction. * ** *I am curious on whether we can get any clue about the year from the branch length of the tree. * *Please comment.* ** *Thanks for the article. Its really nice.* ** *cheers* ** *Srijith * On 2/15/07, Shameer Khadar wrote: > > Have a look at this article : > Baldauf SL: *Phylogeny for the faint of heart: a tutorial.* > *Trends Genet* 2003, *19**:*345-351. > Cheers, > -- > Shameer > On 2/15/07, Shameer Khadar wrote: > > > > Srijith, > > Can you tell me how you created your Phylogram ? > > Is it using the standard Phylogeny protocol MSA -> SEQBOOT (Value) -> > > ProtDist -> Neighbor - Consensus -> Phylogram / Dendrogram ? If that was > the > > case, you will get a picture of evolution based on bootstrap support , > but > > not in terms of year. > > > > PS: I am sorry that your question is not clear to me (may be I didnt get > > what you are looking for :| ). > > > > Cheers, > > Shameer > > NCBS - TIFR > > > > > > On 2/14/07, soorya kiran wrote: > > > > > > Good day all, > > > > > > Can anyone tell how can I find evolutionary distance (Year) from a > given > > > set > > > of amino acid sequences, provided we have constructed the phylogram ? > > > > > > > > > Thanks in advance. > > > > > > Srijith > > > _______________________________________________ > > > General Forum at Bioinformatics.Org - > > > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- P. R. O SooryaKiran Bioinformatics (P) LTD, Industry Incubation Centre, University of Kerala, Karyavattom Campus, Thiruvananthapuram, Keralam, India. 695 581 Ph : +91 (471) 2414593 www.sooryakiran.com Email : kiran.soorya at gmail.com Confidentiality Statement :- The contents of this e-mail, including its attachment, are intended for the exclusive use of the recipient and may contain confidential or privileged information. If you are not the intended recipient, you are strictly prohibited from reading, using, disclosing, copying, or distributing this e-mail or any of its contents. If you received this e-mail in error, please notify the sender by reply e-mail immediately and permanently delete this e-mail and its attachments, along with any copies thereof. Thank you. -- From rajkumar.bondugula at gmail.com Sat Feb 17 00:11:13 2007 From: rajkumar.bondugula at gmail.com (Raj) Date: Fri, 16 Feb 2007 23:11:13 -0600 Subject: [BiO BB] Global sequence alignments Message-ID: <353b2b10702162111w2aabebf6hab6bade5ccf52a29@mail.gmail.com> Hello all, Can any one suggest me a downlodable program to perform global sequence alignment between two protein sequences and give me their sequence identity in percentage? Thank you for your time. Regards, Raj From mourad12345678 at yahoo.com Sun Feb 18 20:51:24 2007 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Sun, 18 Feb 2007 17:51:24 -0800 (PST) Subject: [BiO BB] Call for Papers : ALBIO'07 (Algorithms in Molecular Biology) Message-ID: <78852.8120.qm@web31502.mail.mud.yahoo.com> CALL FOR PAPERS ALBIO'07 Algorithms in Molecular Biology Session of BIOCOMP'07 The 2007 International Conference on Bioinformatics & Computational Biology Monte Carlo Resort, Las Vegas, Nevada, USA (June 25-28, 2007) www.worldacademyofscience.org/worldcomp07/ws/BIOCOMP07 Computational Molecular Biology has emerged from the Human Genome Project as an important discipline for academic research and industrial application. The growing size of biological databases, the complexity of biological problems and the necessity to deal with errors in biological sequences all result in large run time and memory requirements. Biological sequence databases are growing at an exponential rate. All of these factors will make the development of fast, low memory requirements and high-performances algorithms increasingly important in Computational Molecular Biology. In our session, we are interested in papers that deal with all aspects of algorithms in Molecular Biology. We are, particularly, interested in algorithms that address fundamental and/or applied problems in Molecular Biology that are computationally efficient, that have been implemented and experimented on simulated and/or on real biological sequences and that provide interesting new results. The submitted papers should present recent research results and identify and explore directions for future research. Topics include, but not limited to: (i) strings processing, (ii) biological sequences comparison, (iii) structures prediction, (iv) phylogeny reconstruction, (v) DNA sequences assembly, clustering, and mapping, (vi) molecular evolution, (vii) genes prediction/recognition, (viii) genes expression (ix) haplotyping (x) genomes rearrangement. INSTRUCTIONS TO AUTHORS You are invited to submit a draft paper in Word or PDF format, about 5 to 8 pages including figures and references, before March 15, 2007 to the Session Chair : Dr. Mourad Elloumi : E.Mail: Mourad.Elloumi at fsegt.rnu.tn or Mourad12345678 at yahoo.com Important Dates March 15, 2007 : Draft paper (about 5 to 8 pages) submissions due March 31, 2007 : Notification of acceptance April 20, 2007 : Final camera-ready papers & pre-registration due June 25-28, 2007 : BIOCOMP'07 Conference ____________________________________________________________________________________ Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091 From paolo.romano at istge.it Mon Feb 19 07:57:29 2007 From: paolo.romano at istge.it (Paolo Romano) Date: Mon, 19 Feb 2007 13:57:29 +0100 Subject: [BiO BB] Final Call for Papers NETTAB 2007 Message-ID: <7.0.1.0.0.20070219135721.01b8ee40@istge.it> ================================= Apologies, if you're receiving multiple copies ================================= Final Call for Papers 7th International Workshop NETTAB 2007 June 12-15, 2006 Department of Computer Science, University of Pisa, Pisa http://www.nettab.org/2007/ FOCUS THEME A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications ADJUNCT THEMES Algorithms in bioinformatics Formal Methods for Systems Biology Network Tools and Applications in Bioinformatics AIMS This workshop aims at getting together biologists, bioinformaticians, computer scientists and linguists to try to answer the following questions: - Is the Semantic Web of some use for Bioinformatics? - Which goals should have a Semantic Web for Bioinformatics? - Which standards, technologies and tools of the Semantic Web can most profitably be used in Bioinformatics? - Which application did the Semantic Web already find in Bioinformatics? - Which current Bioinformatics research problems can be solved by the Semantic Web? - Which are the short, medium and long term perspectives in applying Semantic Web technologies to Bionformatics? The workshop also intends to: - introduce the basic knowledge of related standards and technologies, in a non trivial way through invited lectures and tutorials - outline the promising features of the Semantic Web in bioinformatics through invited lectures and open discussion - show some valuable examples in bioinformatics through invited lectures, oral communications and posters - support as much discussion as possible through open discussions and a panel discussion - practically demonstrate "how it works" through tutorials INVITED SPEAKERS We are extremely glad to inform you that four excellent speakers have accepted to give an invited lecture at next NETTAB workshop. + Session on Goals of the Semantic Web in Bioinformatics Invited speaker: Eric Neumann, Co-chair of the Health Care and Life Science Interest Group of the Semantic Web Activity at W3C & Teranode Inc., USA + Session on Semantic Web Standards and Technologies Invited speaker: Guus Schreiber, Chair of Semantic Web Deployment Interest Group at W3C & University of Amsterdam, The Netherlands + Session on Semantic Web Tools Invited speaker: Olivier Bodenreider, Medical Ontology Research, National Library of Medicine, USA + Session on Applications of Semantic Web in Bioinformatics Invited speakers: Michael Schroeder, Biotec TU Dresden, Germany, and Albert Burger, Heriot-Watt University, Scotland, UK Titles of the lectures will soon be announced. TOPICS NETTAB workshops also include general sessions on Network Tools and Applications in Biology and adjunct focus topics selected by local organizers. You are therefore welcome to submit your work on any of the followings topics: Goals of a Semantic Web for Bioinformatics: Standards, Technologies, Tools for the Semantic Web Systems for a Semantic Web for Bioinformatics: Existing and perspective applications of the Semantic Web for Bioinformatics Algorithms in Bioinformatics Formal Methods for Systems Biology Network Tools and Applications in Bioinformatics DEADLINES Submission of oral communications: March 16, 2007 Proposals for tutorials: March 16, 2007 Submission of posters: April 20, 2007 Early Registration Deadline: April 27, 2007 SUBMISSION OF CONTRIBUTIONS You are welcome to submit your contributions through the MyReview system at the following URL: http://www.nettab.org/2007/myreview/ . This is a two steps submission procedure. You will have to submit first an abstract and later the paper. You are invited to prepare your contribution according to instructions available at http://www.biomedcentral.com/bmcbioinformatics/ifora/ (specially, see "Preparing main manuscript text" section). See the workshop's web site for more details about the preparation of the papers. PUBLICATION OF PAPERS AND POSTERS All accepted oral communications and posters will be published in the Workshop's Proceedings that will be distributed to all participants. Selected papers will be published by BMC Bioinformatics as a Supplement Issue. When submitting, you will be asked if your submission is intended for the workshop only or for the publication in BMC Bioinformatics too. The papers will be reviewed by the members of the Programme Committee. They will decide whether the papers are accepted for the workshop only or for the publication in BMC Bioinformatics as well. The workshop will engage itself to pay part of the cost of the publication, but please be advised that depending on the final budget of the workshop you could be requested to contribute to publication costs which has been set to 600 British pounds per paper. For any further information or clarification, please contact the organization by email at info at nettab.org . CHAIRS P. Romano, Bioinformatics, Natl Cancer Research Inst., Italy M. Schr?der, Biotechnology Centre, TU Dresden, Germany N. Cannata, Mathematics & Computer Science Dept, Univ. of Camerino, Italy O. Signore, ISTI, National Research Council, Italy PROGRAMME COMMITTEE G. Armano, Electrical and Electronic Engineering Dept, Univ. of Cagliari, IT C. Baker, Institute for Infocomm Research (I2R), SG P. Barahona, Department of Informatics, New University of Lisboa, PT L. Barrio-Alvers, Transinsight GmbH, DE O. Bodenreider, National Library of Medicine, USA A. Burger, Department of Computer Science, Heriot-Watt University, UK M. Cannataro, Experimental and Clinical Medicine Dept, Univ. of Catanzaro "Magna Graecia", IT W. Ceusters, Bioinformatics and Life Sciences, University at Buffalo, USA M. Cockerill, BioMed Central, UK M.-D. Devignes, LORIA, Vandoeuvre les Nancy, FR R. Dieng, INRIA, Sophia Antipolis, FR L. Grivell, European Molecular Biology Organisation, DE M. Harris, European Bioinformatics Institute, UK M. Helmer-Citterich, Biology Dept, University of Rome "Tor Vergata", IT C. M. Keet, Computer Science Faculty, Free University of Bozen-Bolzano, IT J. Koehler, Biomathematics and Bioinformatics, Rothamsted Research, UK M. Krallinger, Spanish National Cancer Research Center (CNIO), ES L. Krippahl, Department of Informatics, New University of Lisboa, PT P. Lambrix, Computer and Information Science Dept, Link?ping University, SE U. Leser, Institute for Computer Science, Humboldt-University of Berlin, DE J. Luciano, Department of Genetics, Harvard Medical School, USA R. Marangoni, Computer Science Department, University of Pisa, IT M. Marchiori, Pure and Applied Mathematics Dept, University of Padua, IT M. Masseroli, Department of BioEngineering, Polytechnic of Milan, IT G. Mauri, Informatics Systems and Communication Dept, Univ. Milan "Bicocca", IT E. Merelli, Mathematics and Computer Science Dept, University of Camerino, IT S. Moeller, Institute of Neuro- and Bioinformatics, University of L?beck, DE S. Philippi, Institute for Software Technology, Univ. of Koblenz-Landau, DE D. Quann, IBM Software Group, USA D. Rubin, Stanford Medical Informatics, Stanford University Medical Center, USA S.-A. Sansone, European Bioinformatics Institute, UK M. Senger, International Rice Research Institute, PH D. Turi, School of Computer Science, University of Manchester, UK G. Vetere, IBM Center for Advanced Studies of Rome, IT D. Zaccagnini, Language and Computing, USA Looking forward to seeing you all in Tuscany. Best regards. On behalf of the Chairs and of the Organizing Committee Paolo Romano Paolo Romano (paolo.romano at istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From marchywka at hotmail.com Mon Feb 19 16:31:20 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 19 Feb 2007 16:31:20 -0500 Subject: [BiO BB] Global sequence alignments In-Reply-To: <353b2b10702162111w2aabebf6hab6bade5ccf52a29@mail.gmail.com> Message-ID: I'm still using clustalw- I even have scripts to parse the output. Also, to reply to earlier poster on data interaction, apparently R does have source code- if it does something close to what you want it may be realistic to modify the code or make your own contributed piece. Sorry for lack of alphabetical order but I also downloaded O- has anyone used this to model cavities? I couldn't quite figure it out and thought there may be some good examples of better suggestions. I also am surprised how easy it is to do simple things with openGL ( as per someone's suggestion earlier). It was pretty easy to write a simple atom class, read a pdb file to populate an STL container of atoms, read a radius file from the O distribution, and quickly make a solid model similar to RasMol. The nice thing about this is that now I can perform operations on the atom collection, generate a new collection of pseudo-atoms ( test spheres that fill a cavity for example ) and then display my calculated "molecule." I'm sure there are packages for this but it doesn't take long before you wish the calculations were done in optimized native code- so C++ with the STL library and openGL works pretty well. If you want to try something like this with a windoze system and no tools, consider downloading cygwin- pymol won't build easily but most of these other things will. ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only >From: Raj >Reply-To: "General Forum at Bioinformatics.Org" > >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Global sequence alignments >Date: Fri, 16 Feb 2007 23:11:13 -0600 > >Hello all, > Can any one suggest me a downlodable program to perform global >sequence alignment between two protein sequences and give me their >sequence identity in percentage? > >Thank you for your time. > >Regards, >Raj >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Want a degree but can't afford to quit? Top school degrees online - in as fast as 1 year http://forms.nextag.com/goto.jsp?url=/serv/main/buyer/education.jsp?doSearch=n&tm=y&search=education_text_links_88_h288c&s=4079&p=5116 From marty.gollery at gmail.com Mon Feb 19 16:42:28 2007 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 19 Feb 2007 13:42:28 -0800 Subject: [BiO BB] Global sequence alignments In-Reply-To: <495B86023F645E4AA009D384E5CAD5C13AF9C4@UNRX1.unr.edu> References: <495B86023F645E4AA009D384E5CAD5C13AF9C4@UNRX1.unr.edu> Message-ID: I believe that 'Needle' from EMBOSS will do this for you, Raj. Marty On 2/19/07, Raj wrote: > Hello all, > Can any one suggest me a downlodable program to perform global > sequence alignment between two protein sequences and give me their > sequence identity in percentage? > > Thank you for your time. > > Regards, > Raj > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS334 775-784-7042 ----------- From skhadar at gmail.com Mon Feb 19 22:52:15 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Tue, 20 Feb 2007 09:22:15 +0530 Subject: [BiO BB] Global sequence alignments In-Reply-To: <353b2b10702162111w2aabebf6hab6bade5ccf52a29@mail.gmail.com> References: <353b2b10702162111w2aabebf6hab6bade5ccf52a29@mail.gmail.com> Message-ID: Hi, Try MALIGN by M.S. Johnson and you can obtain the %ID from the alignment results itself. If you dont have access to MAIGN, create ur alignment using any standard tool and check the alignment statistics using ALISTAT (Part of Eddy's HMMER) cheerSSS!!! -- Shameer Khadar NCBS - TIFR On 2/17/07, Raj wrote: > > Hello all, > Can any one suggest me a downlodable program to perform global > sequence alignment between two protein sequences and give me their > sequence identity in percentage? > > Thank you for your time. > > Regards, > Raj > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From keshet1 at umbc.edu Fri Feb 23 12:54:44 2007 From: keshet1 at umbc.edu (Ben Keshet) Date: Fri, 23 Feb 2007 12:54:44 -0500 Subject: [BiO BB] Cellular Automaton to Simulate Protein Aggregation In-Reply-To: Message-ID: <001c01c75773$b3461a80$29ad5582@umbc80a173302c> Hi everybody, Does anyone know any work done to simulate protein aggregation (or other aggregation processes) using cellular automaton? I found only few papers so far. Does anyone have any personal experience with cellular automaton method in the context of aggregation? Thank you, BK From yzhang at vbi.vt.edu Sun Feb 25 15:02:48 2007 From: yzhang at vbi.vt.edu (yzhang at vbi.vt.edu) Date: Sun, 25 Feb 2007 15:02:48 -0500 (EST) Subject: [BiO BB] anyone know how to get the promoter sequence of mouse gene Message-ID: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> anyone know if I have a mouse gene(or human gene)'s gene accession #, how could I use this number to get promotor sequence of this gene? or -1000bp sequence? How about batch query? best yan From maximilianh at gmail.com Tue Feb 27 09:32:58 2007 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Tue, 27 Feb 2007 15:32:58 +0100 Subject: [BiO BB] anyone know how to get the promoter sequence of mouse gene In-Reply-To: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> References: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> Message-ID: <76f031ae0702270632t2bd41a4yaa1700b3468abd31@mail.gmail.com> googling for mouse and promoter gives you this as first hit: http://rulai.cshl.edu/CSHLmpd2/ batch queries are possible as far as I remember. cheers, Max On 25/02/07, yzhang at vbi.vt.edu wrote: > anyone know if I have a mouse gene(or human gene)'s gene accession #, how > could I use this number to get promotor sequence of this gene? or -1000bp > sequence? How about batch query? > best > yan > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From nuin at terra.com.br Tue Feb 27 09:31:37 2007 From: nuin at terra.com.br (Paulo Nuin) Date: Tue, 27 Feb 2007 09:31:37 -0500 Subject: [BiO BB] anyone know how to get the promoter sequence of mouse gene In-Reply-To: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> References: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> Message-ID: <45E440C9.9010204@terra.com.br> Hi Depending on the number of sequences you have you can do it manually/semi-automatically on the UCSC Genome Browser->Table Browser and modify the parameters to get the sequence. You can upload a list of IDs and then select the amount of upstream you need. 1- Select upload IDs 2- Change output to sequence in the combo box 3- Select what type of sequence you need 4- modify sequence output parameters accordingly HTH Paulo yzhang at vbi.vt.edu wrote: > anyone know if I have a mouse gene(or human gene)'s gene accession #, how > could I use this number to get promotor sequence of this gene? or -1000bp > sequence? How about batch query? > best > yan > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > E-mail classificado pelo Identificador de Spam Inteligente Terra. > Para alterar a categoria classificada, visite > http://mail.terra.com.br/protected_email/imail/imail.cgi?+_u=pnuin&_l=1,1172586137.192834.6651.alcala.hst.terra.com.br,5068,Des15,Des15 > > Esta mensagem foi verificada pelo E-mail Protegido Terra. > Scan engine: McAfee VirusScan / Atualizado em 26/02/2007 / Vers?o: 5.1.00/4971 > Proteja o seu e-mail Terra: http://mail.terra.com.br/ > > > From lixue at iastate.edu Tue Feb 27 09:48:23 2007 From: lixue at iastate.edu (Li Xue) Date: Tue, 27 Feb 2007 08:48:23 -0600 Subject: [BiO BB] anyone know how to get the promoter sequence of mouse gene In-Reply-To: <76f031ae0702270632t2bd41a4yaa1700b3468abd31@mail.gmail.com > References: <2681.198.82.30.149.1172433768.squirrel@webmail.vbi.vt.edu> <76f031ae0702270632t2bd41a4yaa1700b3468abd31@mail.gmail.com> Message-ID: <200702271448.l1REmcVY014901@mailhub-4.iastate.edu> Hi Yan, The following link is to predict promoter region for barley probeset. It is different from your problem in that servers offered are mainly plant genome, but may offer some clue of the steps. http://gremlin1.gdcb.iastate.edu/~volker/teaching/bcb594.html Li At 08:32 AM 2/27/2007, you wrote: >googling for mouse and promoter gives you this as first hit: >http://rulai.cshl.edu/CSHLmpd2/ >batch queries are possible as far as I remember. > >cheers, >Max >On 25/02/07, yzhang at vbi.vt.edu wrote: >>anyone know if I have a mouse gene(or human gene)'s gene accession #, how >>could I use this number to get promotor sequence of this gene? or -1000bp >>sequence? How about batch query? >>best >>yan >> >>_______________________________________________ >>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From yousefim at interchange.ubc.ca Tue Feb 27 11:54:06 2007 From: yousefim at interchange.ubc.ca (Masoud Yousefi) Date: Tue, 27 Feb 2007 08:54:06 -0800 (PST) Subject: [BiO BB] plotting antigenicity or likelihood to stimulate an immune response Message-ID: <2952908.1172595246425.JavaMail.myubc2@handel.my.ubc.ca> Hi All Does anybody know a program that can be used to plot antigenicity or likelihood to stimulate an immune response? We have a package of sequences, the DSE sequences, and we would like to plot the antigenicity of these peptides. We expect to see some kind of linear plot, or average score over amino acids chosen from a moving window across the sequence (the longest sequence is 16 amino acids or so, so we'd like to know which 5 or 6 amino acid sequences from there are antigenic). Cheers M. -- Masoud Yousefi Senior Statistical Analyst Cashman Lab Brain Research Centre University of British Columbia 2211 Wesbrook Mall, Vancouver, BC, V6T 2B5 E-mail: masoud.yousefi at ubc.ca Tel: (604) 827-3307 Fax: (604) 822-7299 From idoerg at burnham.org Wed Feb 28 16:03:16 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 28 Feb 2007 13:03:16 -0800 Subject: [BiO BB] Announcement: AFP - BioSapiens Joint SIG at ECCB 2007 Message-ID: <45E5EE14.80206@burnham.org> Joint AFP-Biosapiens SIG http://2007.BioFunctionPrediction.org The Automated Function Prediction (AFP) SIG and the Biosapiens European network of excellence are teaming up to hold a two-day Special Interest Group (SIG) meeting July 19-20, 2007 alongside ISMB/ECCB 2007. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through predicting the function form protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a SIG that will deal with a wide scope of gene, protein, and genomic annotations. For more information: http://2007.BioFunctionPrediction.org Talks are sought in, but not limited to: * Various aspects of gene and protein function prediction o Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity. o Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss. o Phylogeny based methods o Function from molecular interactions o Function from structure o Function prediction using combined methods o "Meta-talks" discussing the limitations and horizons of computational function prediction. o Assessing function prediction programs * Genomic annotation o Gene finding o Genome visualization o Collaborative annotation o Cooperation between experimental and computational biologists Confirmed speakers include: * Janet Thornton, European Bioinformatics Institute, Cambridge, UK * David Jones University College, London, UK * Rob Russell EMBL, Heidelberg, Germany * Christine Orengo, University College London, UK * Alfonso Valencia, Centro Nacional de Biotecnologia, Madrid, Spain * Ewan Birney, European Bioinformatics Institute, Cambridge, UK * Shoshana Wodak, University of Toronto, Canada * Russ Altman, Stanford University, USA Organizers: Iddo Friedberg, Burnham Institute for Medical Research Adam Godzik, Burnham Institute for Medical Research and University of California, San Diego Christine Orengo, University College, London Important dates: May 1 2007: Talk and poster abstracts due May 21 2007: notification of acceptance May 28, 2007: final abstracts due July 19-20, 2007: AFP-Biosapiens SIG alongside ISMB/ECCB 2007 in Vienna, Austria. Contact us: afp.biosap.2007 at gmail.com For more information: http://2007.BioFunctionPrediction.org -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 http://iddo-friedberg.org http://BioFunctionPrediction.org From mourad12345678 at yahoo.com Wed Feb 28 20:43:18 2007 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Wed, 28 Feb 2007 17:43:18 -0800 (PST) Subject: [BiO BB] Call for Papers : ALBIO'07 (Algorithms in Molecular Biology) Message-ID: <68981.173.qm@web31501.mail.mud.yahoo.com> CALL FOR PAPERS ALBIO'07 Algorithms in Molecular Biology Session of BIOCOMP'07 The 2007 International Conference on Bioinformatics & Computational Biology Monte Carlo Resort, Las Vegas, Nevada, USA (June 25-28, 2007) www.worldacademyofscience.org/worldcomp07/ws/BIOCOMP07 Computational Molecular Biology has emerged from the Human Genome Project as an important discipline for academic research and industrial application. The growing size of biological databases, the complexity of biological problems and the necessity to deal with errors in biological sequences all result in large run time and memory requirements. Biological sequence databases are growing at an exponential rate. All of these factors will make the development of fast, low memory requirements and high-performances algorithms increasingly important in Computational Molecular Biology. In our session, we are interested in papers that deal with all aspects of algorithms in Molecular Biology. We are, particularly, interested in algorithms that address fundamental and/or applied problems in Molecular Biology that are computationally efficient, that have been implemented and experimented on simulated and/or on real biological sequences and that provide interesting new results. The submitted papers should present recent research results and identify and explore directions for future research. Topics include, but not limited to: (i) strings processing, (ii) biological sequences comparison, (iii) structures prediction, (iv) phylogeny reconstruction, (v) DNA sequences assembly, clustering, and mapping, (vi) molecular evolution, (vii) genes prediction/recognition, (viii) genes expression (ix) haplotyping (x) genomes rearrangement. INSTRUCTIONS TO AUTHORS You are invited to submit a draft paper in Word or PDF format, about 5 to 8 pages including figures and references, before March 15, 2007 to the Session Chair: Dr. Mourad Elloumi : E.Mail: Mourad.Elloumi at fsegt.rnu.tn or Mourad12345678 at yahoo.com Important Dates March 15, 2007 : Draft paper (about 5 to 8 pages) submissions due March 31, 2007 : Notification of acceptance April 20, 2007 : Final camera-ready papers & pre-registration due June 25-28, 2007 : BIOCOMP'07 Conference ____________________________________________________________________________________ Expecting? Get great news right away with email Auto-Check. 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