Links to Bioinformatics Databases and Tools

search engines

EBI bioinformatics search
Google
Yahoo!
Infoseek

general reference

Wentian Li's site at Rockefeller

databases

primary databases

GenBank
protein sequences: SWISS-PROT/TrEMBL
protein structure: PDB WWW Server

genome databases

a list of sequenced genomes

E. coli

E. coli Genome/Univ. Wisconsin-Madison
E Coli database/Pasteur Institute
RegulonDB DataBase

S. cerevisae

Saccharomyces Genome Database
Yeast Promoter Database
Yeast regulatory sequence analysis
MIPS Protein-Protein Interaction Table

C. elegans

The Sanger Centre : C. elegans Project
WU GSC: C. elegans
WormBase - Home Page

Drosophila

Berkeley Drosophia Genome Project databases
FlyBase @ flybase.bio.indiana.edu

human genome

Human Genome-NCBI
Human Genome-UCSC

derived databases and other specialized sources

Eukaryotic Promoter Database
TRANSFAC - The Transcription Factor Database
PROSITE - Database of protein families and domains
BLOCKS database
Pfam - database of protein domains and HMMs

tools

sequence alignment and trees

Smith-Walterman at EBI/EMBL
BLAST at NCBI
Fasta3
ClustalW - multiple sequence alignment
A List of Phylogeny Programs
PHYLIP - one of the most popular phylogeny programs

gene finding

a list of gene finding algorithms
New GENSCAN Web Server at MIT
GrailEXP: A System for the Computational Analysis of DNA Sequence
BCM gene finder

motif search

MEME - Introduction
The Gibbs Motif Sampler Homepage
CONSENSUS
ftp site to download CONSENSUS