Web document 5.1. Organism-Specific BLAST and FASTA Sites

 

These sites provide access to databases with sequences that are not available in standard NCBI BLAST searches. Some use the WU BLAST 2.0 algorithm (described below)

Organism

Description

URL

Bacteria

Cyanobase (Cyanobacteria)

http://bacteria.kazusa.or.jp/cyanobase/

Dictyostelium discoideum

Dicty blast

http://dicty.sdsc.edu/

 

D. discoideum Genome Project

http://genome.imb-jena.de/dictyostelium/BlastDictyForm.html

Fungi

 

 

Schizosaccharomyces pombe

The Wellcome Trust Sanger Institute

http://www.sanger.ac.uk/Projects/S_pombe/blast_server.shtml

Aspergillus fumigatus

The Wellcome Trust Sanger Institute

http://www.sanger.ac.uk/Projects/A_fumigatus/

Candida albicans

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/C_albicans/blast_server.shtml

Neurospora crassa

Whitehead Institute

► http://www-genome.wi.mit.edu/annotation/fungi/neurospora/

Pneumocystis carinii

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/P_carinii/blast_server.shtml

Saccharomyces cerevisiae

MIPS

► http://mips.gsf.de/cgi-bin/blast/blast_page?genus=yeast

White rot

Department of Energy Joint Genome Institute

► http://www.jgi.doe.gov/programs/whiterot/whiterot_mainpage.html

Insect

 

 

Drosophila melanogaster

FlyBLAST

► http://www.fruitfly.org/blast/

Mosquito

An NCBI BLAST of culicidae from the Mosquito Genomics WWW server (http://klab.agsci.colostate.edu/)

► http://mosquito.colostate.edu/cgi-bin/ace/blast/MsqDB

Anopheles gambiae

AnoDB

► http://konops.imbb.forth.gr/cgi-bin/blast2.pl

Microbial Genomes Various

Allows BLAST of both completed and unfinished genomes

► http://www.ncbi.nlm.nih.gov/BLAST/

 

Allows BLAST of both completed and unfinished genomes

http://www.tigr.org

 

Comprehensive microbial resource at the J. Craig Venter Institute (JCVI) (formerly TIGR)

► http://tigrblast.tigr.org/cmr-blast/

 

Dozens of organism-specific BLAST searches

► http://www.sanger.ac.uk/Projects/Microbes/

Parasites

 

 

Various

At EBI

► http://www.ebi.ac.uk/blast2/parasites.html

 

From the Oswaldo Cruz Institute, Brazil

► http://www.dbbm.fiocruz.br/genome/parasite-genome/parasite_blast_server.html

Phytophthora

A plant pathogen studied at http://www.ncgr.org

► http://www.ncgr.org/pgc/blast/blast.html

Plants: Arabidopsis thaliana

Thale cress

► http://genome-www2.stanford.edu/cgi-bin/AtDB/nph-blast2atdb

Protozoa

 

 

Babesia bovis

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/B_bovis/blast_server.shtml

Giardia lamblia

Marine Biological Laboratory, Woods Hole

► http://www.mbl.edu/Giardia/blast.html

Plasmodium chabaudi

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/P_chabaudi/blast_server.shtml

Plasmodium falciparum

This is the organism that causes malaria

► http://www.ncbi.nlm.nih.gov/BLAST/

 

Plasmodium genome resource

► http://plasmodb.org/

 

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/P_falciparum/blast_server.shtml

Tetrapygus niger

Sea urchin BLAST

► http://sea-urchin.caltech.edu/genome/sequence/blast.py

Various organisms

TIGR BLAST

► http://www.tigr.org

 

OnmiBLAST server at The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/DataSearch/omniblast.shtml

 

The Gene2EST BLAST server

► http://woody.embl-heidelberg.de/gene2est/

 

The oral BLAST server

► http://199.93.248.241/blast/blast.html

Vertebrate

 

 

Ciona intestinalis

Sea squirt

► http://www.jgi.doe.gov/programs/ciona/ciona_mainpage.html

Danio rerio

Zebrafish at The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/D_rerio/blast_server.shtml

Fugu

Includes Fugu (the pufferfish) and zebrafish

► http://fugu.hgmp.mrc.ac.uk/blast/

 

Department of Energy Joint Genome Institute

► http://www.jgi.doe.gov/programs/fugu/fugu_mainpage.html

Gallus gallus

From ChickMap ► (http://www.ri.bbsrc.ac.uk/chickmap/ChickMapHomePage.html)

► http://www.ri.bbsrc.ac.uk/cgi-bin/est-blast/blast.pl

Homo sapiens

Allows searches against specific chromosomes

http://www.ncbi.nlm.nih.gov/BLAST/

 

Premiere human genome site

► http://www.Ensembl.org

Mus musculus

Chromosome-specific mouse BLAST

► http://www.ncbi.nlm.nih.gov/genome/seq/MmBlast.html

 

Mouse Genome Informatics at Jackson Laboratories

► http://mouseblast.informatics.jax.org/prototype/

 

The Wellcome Trust Sanger Institute and Ensembl

► http://mouse.Ensembl.org/

 

The Wellcome Trust Sanger Institute

► http://mouse.Ensembl.org/perl/blastview

 

National Institute of Aging

► http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html

Xenopus

Contains data from both X. laevis and X. tropicalis

► http://www.sanger.ac.uk/Projects/X_tropicalis/blast_server.shtml

Worms

 

 

Brugia malayi

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/B_malayi/blast_server.shtml

 

B. Malayi BLAST server

► http://www.dbbm.fiocruz.br/genome/parasite-genome/Brugia_blast_server.html

Caenorhabditis elegans

WormBLAST; also other organisms; Genome Sequencing Center, Washington University

► http://genome.wustl.edu/gsc/Blast/client.pl

C. elegans

The Wellcome Trust Sanger Institute

► http://www.sanger.ac.uk/Projects/C_elegans/blast_server.shtml

C. elegans

Steve Jones’ Genome Project DNA/protein databases

► http://www.bio.ic.ac.uk/fgn/blastform/elegansblast.html

 

 

 Please let me know about broken links, or suggest links to add (email here).

Last updated 28 January, 2010