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Bioinformatics-related links

There are many on-line resources available for the researcher. Many of these were government funded but some are from commerical ventures. Modern biochemistry, molecular biology, and cell biology all make use of these resources extensively. Indeed, even field researchers are finding these resources useful for helping them to answer fundamental questions about the evolution of organisms.

Below is a table that identifies sequence databases as well as websites that contain useful information (such as software or images) for a biology or BMB student.

Major Biological Data and Information Sources
Subject Source Link
Biomedical literature PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
Nucleic acid sequence

GenBank

SRS at EMBL/EBI

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Nucleotide

http://srs.ebi.ac.uk

Genome sequence

Entrez Genome

TIGR databases

GOLD

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Genome

http://www.tigr.org/tdb/

http://wit.integratedgenomics.com/GOLD/

Protein sequence

GenBank

SWISS-PROT at ExPASy

PIR

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Protein

http://www.expasy.ch/spro/

http://www-nbrf.georgetown.edu

Protein structure Protein Data Bank http://www.rcsb.org/pdb/
Entrez Structure DB Protein and peptide mass spectroscopy PROWL

http://prowl.rockefeller.edu

Post-translational modifications RESID http://www-nbrf.georgetown.edu/pirwww/search/textresid.html
Biochemical and biophysical information

ENZYME

BIND

http://www.expasy.ch/enzyme/

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Structure

Biochemical pathways

PathDB

KEGG

WIT

http://www.ncgr.org/software/pathdb/

http://www.genome.ad.jp/kegg/

http://wit.mcs.anl.gov/WIT2/

Microarray Gene Expression Links

http://industry.ebi.ac.uk/~alan/MicroArray/

2D-PAGE SWISS-2DPAGE http://www.expasy.ch/ch2d/ch2d-top.html
Web resources

The EBI Biocatalog

IUBio Archive

http://www.ebi.ac.uk/biocat/

http://iubio.bio.indiana.edu

Ciliate resources

Tetrahymena Genome Project

Paramecium Genome Project

Ciliates in the Classroom

http://www.lifesci.ucsb.edu/~genome/Tetrahymena/index.htm

 

http://aiaia.cgm.cnrs-gif.fr/blast/

 

http://www.wooster.edu/biology/Ciliates/Ciliates_in_the_Classroom.html

Software resources PCR software http://www.highveld.com/pcr.html#pcrs
This table was adapted from Developing Bioinformatics Computer Skills:An Introduction to Software Tools for Biological Applications by C. Gibas and P. Jambeck 2001 O'Reilly & Associates ISBN: 1-56592-664-1 
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Last Updated: August 24, 2004
Dean Fraga dfraga@wooster.edu