Similarity Search Engines

Organism-specific searches | Protein family searches | General database searches | Alerting services

Organism-specific similarity search engines

Eukaryote

Metazoa (Multicellular animals)
- Homo sapiens
  - Human @ WU-St. Louis (St. Louis projects only)
  - Human @ Sanger
  - Tentative Human Consensus @ NCBI-THC
  - Human Gene Index (HGI) @ TIGR
  - Consensus from Human ESTs (STACK) @ SANBI
  - Human dbEST @ NCBI
  - Human BAC ends @ TIGR
- Mus musculus
  - Mouse Gene Index (MGI) @ TIGR
  - Mouse dbEST @ NCBI
- Rattus rattus Rat Gene Index (RGI) @ TIGR
- Danio rerio Zebrafish Gene Index (ZGI) @ TIGR
- Fugu rubripesFugu rubripes @ HGMP/MRC
- Drosophila
- Nematoda
  - All nematode (bar C. elegans) @ EBI-Parasite Genomes
  - Filarial nematode @ EBI-Parasite Genomes
  - Caenorhabditis elegans @ Sanger
  - Caenorhabditis elegans @ WU-St. Louis
  - Caenorhabditis elegans ESTs @ NIG, Japan
  - Caenorhabditis briggsae @ WU-St. Louis
  - Onchocerca volvulus @ EBI-Parasite Genomes
  - Brugia malayi @ EBI-Parasite Genomes
- Schistosoma mansoni and Schistosoma spp. @ EBI-Parasite Genomes
Viridiplantae (Green algae and higher plants) : Seed plants
- Arabidopsis thaliana
  - Arabidopsis thaliana @ Stanford
  - AT (Arabidopsis thaliana) @ TIGR
  - Arabidopsis Gene Index (AGI) @ TIGR
  - Arabidopsis thaliana @ WU-St. Louis (St. Louis projects only)
  - Arabidopsis thaliana @ Kazusa
- Rice Gene Index (OGI) @ TIGR
Fungi
- Saccharomyces cerevisiae
  - Saccharomyces cerevisiae @ Stanford
  - Saccharomyces cerevisiae @ Sanger
  - Saccharomyces cerevisiae @ NCBI
  - Saccharomyces cerevisiae @ MIPS
- Schizosaccharomyces pombe @ Sanger
- Aspergillus nidulans @ OU (Oklahoma University)
- Neurospora crassa @ OU (Oklahoma University)
- Candida albicans @ Sanger
Dictyosteliida (Slime mold) Dictyostelium discoideum cDNA @ CSM
Euglenozoa : Kinetoplastida
- kinetoplastid protozoan @ EBI-Parasite Genomes
- African trypanosome @ EBI-Parasite Genomes
- Trypanosoma brucei @ TIGR
- Trypanosoma cruzi @ EBI-Parasite Genomes
- Leishmania major and Leishmania spp. @ EBI-Parasite Genomes
Alveolata : Apicomplexa
- all Apicomplexa @ EBI-Parasite Genomes
- Toxoplasma gondii @ EBI-Parasite Genomes
- Toxoplasma gondii @ NCBI-Apicomplexan
- Cryptosporidium parvum @ EBI-Parasite Genomes
- Plasmodium falciparum
  - Plasmodium falciparum and Plasmodium spp. @ EBI-Parasite Genomes
  - Plasmodium falciparum @ Sanger
  - Plasmodium falciparum @ NCBI-Apicomplexan
  - Plasmodium falciparum [Chromosome 2]@ NCBI-unfinished microbial genomes or @ NCBI-TIGR

Archae

Euryarchaeota

Bacteria

Cyanobacteria Synechocystis sp. PCC 6803 @ CyanoBase
Cytophagales (Green sulphur bacteria) Porphyromonas gingivalis W83@ NCBI-unfinished microbial genomes
Firmicutes (Gram positive bacteria)
- Actinomycetes
  - M. leprae, M. tuberculosis and M. smegmatis @ MycDB
  - Mycobacterium leprae @ Sanger
  - Mycobacterium tuberculosis CSU#93 @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
  - Mycobacterium tuberculosis H37Rv @ NCBI-unfinished microbial genomes or @ Sanger
  - Mycobacterium tuberculosis @ SANBI
  - Streptomyces coelicolor @ Sanger
- Clostridium group
  - Bacillus subtilis @ Institut Pasteur
  - Clostridium acetobutylicum ATCC824@ NCBI-unfinished microbial genomes
  - Enterococcus faecalis @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
  - Mycoplasma genitalium @ TIGR
  - Staphylococcus aureus @ OU (Oklahoma University)
  - Staphylococcus aureus @ NCBI-unfinished microbial genomes or @ NCBI-OU
  - Streptococcus pyogenes @ OU (Oklahoma University)
  - Streptococcus pyogenes @ NCBI-unfinished microbial genomes or @ NCBI-OU
  - Streptococcus pneumoniae @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
Green non-sulfur bacteria Deinococcus radiodurans @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
Proteobacteria
- alpha subdivision
  - Rhodobacter capsulatus @ University of Chicago
- beta subdivision
  - Neisseria gonorrhoeae @ NCBI-unfinished microbial genomes or @ NCBI-OU
  - Neisseria gonorrhoeae @ OU (Oklahoma University)
  - Neisseria meningitidis MC58 @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
  - Neisseria meningitidis serogroup A @ NCBI-unfinished microbial genomes or @ Sanger
- gamma subdivision
  - Actinobacillus actinomycetemcomitans @ OU (Oklahoma University)
  - Actinobacillus actinomycetemcomitans @ NCBI-unfinished microbial genomes or @ NCBI-OU
  - Escherichia coli @ NCBI
  - Haemophilus influenzae @ TIGR
  - Pseudomonas aeruginosa @ NCBI-unfinished microbial genomes or @ NCBI-PAGP
  - Salmonella typhimurium and Salmonella typhi @ WUStL - Bacterial Genomes
  - Vibrio cholerae @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
  - Yersinia pestis @ Sanger
- epsilon subdivision
  - Campylobacter jejuni NCTC11168 @ NCBI-unfinished microbial genomes or @ Sanger
  - Helicobacter pylori @ TIGR
Spirochaetales
- Borrelia burgdorferi @ TIGR
- Borrelia burgdorferi @ NCBI-TIGR
- Treponema pallidum @ NCBI-unfinished microbial genomes or @ NCBI-TIGR
Thermotogales Thermotoga maritima @ NCBI-unfinished microbial genomes or @ NCBI-TIGR

Archae and Bacteria through Micado @ Jouy

Mitochondrial sequences @ NCBI

Protein Family Database Search Engines

@ ExPASY: PROSITE

@ ISREC - ProfileScan Server for protein search
or Frame-ProfileScan Server for DNA search: PROSITE profiles; PROSITE Patterns; Pfam A; Gribskov collection

@ Sanger protein search or DNA search: Pfam

@ WUStL protein search: Pfam

@ Toulouse: ProDom

@ FHCRC - Blocks Searcher: Blocks+ Database; Prints Database

@ UCL: Prints/PROSITE

@ Stanford - Identify: Blocks and Prints Databases

@ EMBL-Heidelberg: SMART

@ NCBI: Conserved Domain Database

General Database Search Engines

@ NCBI gapped BLAST and PSI BLAST

@ EMBL gapped BLAST

@ EBI gapped BLAST or Fasta3 or Smith-Waterman

@ ISREC WU-BLAST

@ Institut Pasteur Basic, and advanced BLAST, gapped BLAST and PSI BLAST

@ GENESTREAM CRBM, Montpellier BLAST

@ DDBJ, Japan BLAST, Fasta or SSearch

@ IDEAS, Japan BLAST or Fasta

@ UCL, London BLAST

Alerting Services

Sequence Alerting System @ Heidelberg - performs daily comparisons to new entries in the protein and nucleic acid databanks.
SwissShop @ ExPASY - performs weekly comparisons to new and updated entries in the SwissProt protein databank.
XREFdb @ NCBI - performs monthly comparisons to dbEST and reports which ESTs have been mapped.
AutoBlast @ Sanger Center - performs weekly comparisons to data accumulating from the C.elegans genomic sequencing project.

Last modified 25 August 2000