Bioinformatics & Computational
Biology
| Old Look Web Site |
Site last updated:
02/14/03
CAA
What's New The latest developments in Bioinformatics here and elsewhere
| New |
New Bioinformatics Seminars
All Sessions Free
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Date
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Place
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Topic
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Time
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Tuesday
2/18/03 |
Light Hall 208
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More than just BLAST: Overview of Popular & Innovative Solutions |
3:00-4:30 pm
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Thursday
2/20/03 |
Light Hall 202
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Celera Discovery System and GCG's Wisconsin Package/SeqWeb/SeqLab
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3:00-4:30 pm
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Tuesday
2/25/03 |
Light Hall 214
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Desktop Based Solutions
MacVector, Vector NTI, DS-Gene, Sequencher Custom Solutions |
10:00-11:30 am
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Thursday
2/27/03 |
Light Hall 208
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Incredible Internet Tools including the Genome
Browser
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3:00-4:30 pm
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02/12/03 TIME magazine takes a look at molecular biology.
03/07/01 New look VU Bioinformatics web site. Send comments or feedback to the webmaster.
02/16/01 Human Genome Assembly released by Human Genome Project/Celera in Science
02/15/01 Human Genome Assembly released by International Public Genome Project in Nature. There's also now a nice genome section called The Genome Gateway that is presumably going to be updated on a regular basis.
Archive for news items prior to Jan 1, 2001
Software & Support What's available at Vanderbilt
Vanderbilt has a bioinformatics support specialist on staff. Charles Alexander is available for consultations and training sessions on how to use various bioinformatics software. He is also responsible for the installation and maintenance of the various bioinformatics packages. Vanderbilt's Academic Computing and Information Services (ACIS) also provides vital systems and software support for these services.
There are regularly scheduled workshops to train the user community in the use of bioinformatics applications.
Celera Genomics
Vanderbilt was the first academic institution to enter into an agreement with Celera Genomics to use the Celera Discovery System. Go here for more information.
One major focus of our support is the Genetics Computer Group's (GCG) Wisconsin package. The package consists of over 100 programs that perform DNA/RNA and protein analyses. It is a subscription based service. We've compiled a short introductory list of Frequently Asked Questions or FAQ on the software, as well as, the related services for the Vanderbilt community. If you would like to learn more about the package, please visit GCG's site or contact Charles Alexander.
Sequencher is a very powerful sequence assembly package for the Windows 95/98/NT/2000 and Macintosh platforms. It has the ability to assemble contigs and determine consensus sequences in a friendly and intuitive user environment.
We're currently in discussions with the makers of Sequencher for a group discount/site license agreement
MacVector is a Macintosh based sequence analysis package manufactured and distributed by Oxford Molecular Group, Inc (OxMol). OxMol is the same company that distributes GCG's Wisconsin package. To review some of the features of the package, visit OxMol's website. There is an academic discount program, that is available to the Vanderbilt community. Please contact Vanderbilt bioinformatics support for more information.
OMIGA was positioned by OxMol to be the Windows based equivalent of MacVector. The new release of OMIGA - version 2.0 is a good, solid Windows 95/98/NT desktop based sequence analysis package. There is an academic discount program, that is available to the Vanderbilt community. Please contact Vanderbilt bioinformatics support for more information.
Phil Green's Suite (Phred,Phrap,Consed, RepeatMasker,PolyPhred)
Phil Green at the University of Washington's Molecular Biotechnology Dept. has a suite of programs that are very useful for large scale high throughput sequencing projects. The programs are:
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Phred
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Base calling software that improves the accuracy of the sequence by predicting error probabilities of each base call. |
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Phrap
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Phrap assembles sequences rapidly and estimates the "quality" of consensus sequences. |
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Consed
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X windows based cosensus sequence editor to view finished sequence assemblies in a graphical user interface. |
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RepeatMasker
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Screens DNA for interspersed repeats and low complexity sequences. |
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PolyPhred
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According to the UW-MBT website: "Polyphred is a program for discovering single nucleotide substitution polymorphisms and mutations. The goal of Polyphred is to produce a set of candidate positions which exhibit characteristics consistent with those exhibited by polymorphic positions." |
In order to use the programs above, you need shell (command line) access to GCG. Please write to bioinformatics@vanderbilt.edu for a shell account.
Coming soon!
We're working on installing the C.elegans sequencing project's tools and sequence database locally. in the meantime, use the WebAce interface to AceDB at The Sanger Center. Online Help is available. There's also a corresponding database and associated tools for the human sequences in the AceDB database called humace.
Various computational biology tools available on the Internet.
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| Participants in a Vanderbilt bioinformatics workshop |
New! GCG SeqWeb Sign up is now open for a 2 day GCG SeqWeb workshop to be held on March 13,14 2001 from 9:30 am - 11:30 am.
When: Tuesday, Wednesday, March 13 and 14, 2001
Time: 9:30 am - 11:30 noon
Where: Hill
Center 151 (ACIS Computer Training Room)
Appleton
Place (near 18th Ave. S and Horton Place)
New! Celera Workshop
When: Thursday, March 15, 2001
Time: 9:00 am - 11:30 am
Here's a map. For more information or to sign up, e-mail bioinformatics@vanderbilt.edu
Custom sessions for individual labs and specific needs are also available. Please contact Charles Alexander for further information
The bioinformatics applications server is a Sun UltraServer E450 with a 300 Mhz UltraSparc CPU. The system has 256MBytes of internal memory (RAM) and approximately 20 Gbytes of data storage and user space. The data storage and user space is also mirrored or striped across another 20 Gbytes of disk in case of data corruption or worse, disk failure.
It's BIG - Bioinformatics Interest Group
Informal group of interested parties to meet regularly in the fall. Send mail to bioinformatics@vanderbilt.edu if you want to be updated on this activity. We might even feed you...
Ensembl is an genome assembly viewer and annotation tool and viewer. Covers human and other eukaryotes. Definitely a site you should visit.
Similar to Ensembl but not as sophisticated. It has more current and other kinds of information to supplement the genome assembly. Still very impressive.
The SNP consortium is now one of the best organized SNP resources out there. Also try the dbSNP for completeness in your search.
GenScan is a tool to predict gene structures in your genomic DNA sequence. Works real well for eukaryotes. Also very accurate if the length of your exons are not too short or too long.
A PCR primer prediction program that is probably the best one out there and it's FREE! Also good for sequencing primers (actually it's excellent). Only negative is that it's not the best user interface partly because it gives you so many options and great fine control. Can be a little overwhelming.
National Center for Biotechnology Information - NCBI
"LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accession numbers, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and relevant web sites. " from the NCBI
A one stop hub for all kinds of tools & support in bioinformatics and computational biology
The Institute for Genomic Research has some useful software tools and databases. The annotation in TIGR's databases is much more complete than some Genbank based data. The sequence collection however is not as complete.
Washington University - St. Louis, MO
The Genome Sequencing Center (GSC) at WUStl is one of the major bioinformatics centers in the country. The GSC is part of the Department of Genetics at Washington University at St. Louis, MO. Strong development team is responsible for a lot of innovations in bioinformatics software. Home of PFAM, Protein Family Domains database.
Sanger
The Sanger Center is one of the premier research centers in the world. It is located in the Wellcome Trust Genome Campus near Cambridge, England in the United Kingdom. A unique partnership between the government of the UK and the Glaxo-Wellcome Trust, a private research foundation. Home of some great work in genomics. The campus also hosts the European Bioinformatics Institute and the UK Human Genome Mapping Project Resource Centre (HGMP-RC).
MBCR
The Molecular Biology Computing Resource at Baylor College of Medicine in Houston, Texas. A publicly available search engine is found here. The BCM Search Launcher lets you submit jobs in "batch" mode. There's also a nice list of some tools available on the web that are not included in the BCM Search Launcher.
Stanford
The Stanford Genomics Resources site has great resources and tools for use with the Saccharomyces cerevisiae (yeast) and Arabidopsis thaliana (pea) genomes.
Expasy
The ExPASy site in Switzerland is indispensable has a protein sequence and structure analysis resource. If you perform 2D-PAGE (two dimensional polyacrylamide gel electrophoresis) analyses, you can also find a reference maps database for the identification of different proteins.
EBI/EMBNet
The European
Molecular Biology Laboratory (EMBL) is Europe's largest public and
scientific molecular biology research consortium. The European
Bioinformatics Institute (EBI) is a part of this consortium. The EBI
maintains the data from the EMBL
DNA database. The EMBL offers some useful publicly
accessible services as well.
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Charles
A. Alexander
Vanderbilt University Medical Center
Program in Human Genetics
Computing/Bioinformatics Core
519 Light Hall
Nashville, TN 37232-0700
Tel: (615)322-0855
e-mail:charles.alexander@vanderbilt.edu
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