Databases Database Catalogs
DBCAT - public catalog of databases, at Infobiogen
Helix Systems Scientific Databases - locally available databases

Genomic
UCSC Genome Browser - the gold standard of genome browsers
National Center for Biotechnology Information (NCBI) - clearinghouse for all genomic information
Ensembl - joint project between EBI and Sanger Institute
GDB - The Human Genome Database

Nucleic Acids
GCG-Lite Sequence Lookup - search via GCG-Lite, at Helix Systems (NIH only)
Entrez - The Life Sciences Search Engine, at NCBI
SRS - Sequence Retrieval System, at EBI
dbEST - sequence and mapping data on partial, "single-pass" cDNA sequences or ESTs
NDB - Nucleic Acids Database, at Rutgers
Tumor Gene Database - information about targets for cancer-causing mutations

Proteins
GCG-Lite Sequence Lookup - search via GCG-Lite, at Helix Systems (NIH only)
SwissProt - at ExPASy.org
Entrez - The Life Sciences Search Engine, at NCBI
SRS - Sequence Retrieval System, at EBI
Molecules To Go - text-based interface to the PDB on Helix Systems
MEROPS - The Peptidase Database, at the Wellcome Trust Sanger Institute
Human Mitochondrial Protein Database - multiple query types available, at NIST
HIV Protease Database - at NCI-Frederick

Factors and Motifs
Transfac Prosessional - transcription activation factor database (NIH only)
BIOBASE - free registration required

Enzymes
REBASE - good old New England Biolabs
ENZYME Database - at ExPASy.org
IntEnz - at EBI
Biology-oriented newsgroups - via the local server at Helix Systems

Plasmids
Genome Database of Naturally Occurring Plasmids - 'nuff said
NCCB - simple search engine, Royal Netherlands Acad. of Arts and Sciences, Utrecht

 

Organism-Specific Databases

Mammalian
Mouse Genome Database - synoptic descriptions with bibliographic citations
Portable Dictionary of the Mouse Genome - compact, downloadable database

Worm
Worm Base - biology and genome of C. elegans
Caenorhabditis elegans WWW Server - one-stop shopping for C. elegans

Insect
FlyBase - comprehensive database for genetics and molecular biology of Drosophila
Mosquito Genomics WWW Server - clearinghouse for everything about Mosquito genomics

Yeast
Saccharomyces Genome Database - at Stanford

Fungi
Fungal Genetics Stock Center - stocks, sequences, vectors, strains, and gene libraries

Prokaryote
IECA Database Portal - collection of E. coli servers around the world
SubtiList WWW Server - all about B. subtilis, Pasteur Institute
Entrez Microbial Genomes - 196 completed genomes and counting...

Plants
Arabidopsis Information Resource - very nice gateway to our favorite mustard weed
Grain genes - database for triticaea and avena
The Korea Rice Genome Database - at Myongii University
ChromDB - the plant chromatin database, at University of Arizona

Other
Ribosomal Database Project - at Michigan State University
National Human Genome Research Institute - ongoing research into genomics