Bioinformatics and Functional Genomics

Table 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
Bacteria: Cyanobacteria	Cyanobase (Cyanobacteria)
Bacteria: Streptomyces coelicolor	The Wellcome Trust Sanger Institute
Dictyostelium discoideum	Dicty blast
Dictyostelium discoideum	Dictyostelium discoideum Genome Project
Fungi: Schizosaccharomyces pombe	The Wellcome Trust Sanger Institute
Fungi: Aspergillus fumigatus	The Wellcome Trust Sanger Institute
Fungi: Candida albicans	The Wellcome Trust Sanger Institute
Fungi: Neurospora crassa	Whitehead Institute
Fungi: Pneumocystis carinii	The Wellcome Trust Sanger Institute
Fungi: Saccharomyces cerevisiae	MIPS
Fungi: White rot	Department of Energy Joint Genome Institute
Insect: Drosophila melanogaster	FlyBLAST
Insect: Mosquito	An NCBI BLAST of culicidae from the Mosquito Genomics WWW Server
Insect: Anopheles gambiae	AnoDB
Microbial Genomes: various	Allows BLAST of both completed and unfinished genomes
Microbial Genomes: CMR	Comprehensive microbial resource at TIGR
Microbial Genomes: various	Dozens of organism-specific BLAST searches
Parasites: various	At EBI
Parasites: various	From the Oswaldo Cruz Institute, Brazil
Phytophthora	A plant pathogen studied at http://www.ncgr.org
Protozoa: Babesia bovis	The Wellcome Trust Sanger Institute
Protozoa: Giardia lamblia	Marine Biological Laboratory, Woods Hole
Protozoa: Plasmodium chabaudi	The Wellcome Trust Sanger Institute
Protozoa: Plasmodium falciparum	This is the organism that causes malaria
Protozoa: Plasmodium falciparum	Plasmodium genome resource
Protozoa: Plasmodium falciparum	The Wellcome Trust Sanger Institute
Tetrapygus niger	Sea urchin BLAST
Various organisms	TIGR BLAST
Various organisms	OnmiBLAST server at The Wellcome Trust Sanger Institute
Various organisms	The Gene2EST BLAST Server
Vertebrate: Ciona intestinalis	Sea squirt
Vertebrate: Danio rerio	Zebrafish at The Wellcome Trust Sanger Institute
Vertebrate: Fugu	Includes Fugu (the pufferfish) and zebrafish
Vertebrate: Gallus gallus	From ChickMap
Vertebrate: Homo sapiens	Allows searches against specific chromosomes
Vertebrate: Homo sapiens	Premiere human genome site
Vertebrate: Mus musculus	Mouse Genome Informatics at the Jackson Labs
Vertebrate: Mus musculus	The Wellcome Trust Sanger Institute and Ensembl
Vertebrate: Mus musculus	The Wellcome Trust Sanger Institute
Vertebrate: Mus musculus	National Institute of Aging
Vertebrate: Xenopus	Contains data from both Xenopus laevis and Xenopus tropicalis
Worms: Brugia malayi	The Wellcome Trust Sanger Institute
Worms: Brugia malayi	Brugia Malayi Blast Server
Worms: C. elegans	WormBLAST; also other organisms; Genome Sequencing Center, Wash. U.
Worms: C. elegans	The Wellcome Trust Sanger Institute

 

Table 5-2. Molecule-specific BLAST and BLAST-related sites. These sites provide
databases of particular molecules for selected searches

Molecule	Description
Immunoglobulins	IgBLAST
MS BLAST	Mass spectrometry driven BLAST (WU BLAST 2.0)
Proteins	Network Protein Sequence Analysis at Pole Bio-Informatique Lyonnais
Proteins	EMBnet-CH BLAST Network Service
Proteins	PRODOM BLAST with graphical output (Toulouse)
Single nucleotide polymorphisms (SNPs)	At NCBI
Transcript assembly program	EST-based gene finder (WU BLAST 2.0)
Vectors (VecScreen)	Useful to detect vector contamination of sequences

 

Table 5-3. Specialized BLAST algorithms and distinct BLAST-related algorithms available on the world wide web. Abbreviations: NCBI refers to http://www.ncbi.nlm.nih.gov/BLAST/. DDBJ refers to search tools at the DNA Database of Japan (http://www.ddbj.nig.ac.jp/E-mail/homology.html).

Algorithm	Description
PSI-BLAST	Position Specific Interated BLAST
PHI-BLAST	Pattern hit initiated BLAST
MegaBLAST	For large DNA queries
RPS-BLAST	See Chapter 6
NCBI BLAST2	EMBL/European Bioinformatics Institute
FASTA3	EMBL/European Bioinformatics Institute
WU-BLAST 2.0	EMBL/European Bioinformatics Institute
WU-BLAST 2.0	EMBL
WU-BLAST 2.0	Genome Sequencing Center, Washington U.
WU-BLAST 2.0	Institut Pasteur
WU-BLAST 2.0	Mouse Genome Informatics at Jackson Labs
WU-BLAST 2.0	Transcript assembly program
WU-BLAST 2.0	The Institute for Genomic Research
BLAST	Swiss Institute of Bioinformatics and the Swiss Center for Scientific Computing
FASTA	DNA Database of Japan
BLAST	DNA Database of Japan
SSEARCH	DNA Database of Japan
PSI-BLAST	DNA Database of Japan
FASTA	From the University of Virginia (Bill Pearson)
SSEARCH	From the University of Virginia (Bill Pearson)
BSU	BLAST search updater
MSPcrunch	Used for analysis of BLAST results

 

Table 5-4. Results of a PSI-BLAST search with human retinol-binding protein (NP_006735). Iteration 1 represents the initial search results, comparable to a standard blastp search result. Subsequent PSI-BLAST iterations provide a dramatic rise in the number of database hits above threshold (E = 0.005). Further iterations do not result in substantially different results than seen in iteration 12.

Iteration	Number of hits	Hits above threshold	Newly Added	Fell Below threshold
1	104	49	--	--
2	173	96	48	1
3	236	178	85	3
4	301	240	64	2
5	344	283	43	0
6	342	298	17	2
7	378	310	12	0
8	382	320	11	1
9	391	320	11	1
10	372	336	8	2
11	370	337	2	1
12	371	338	1	0

 

Table 5-5. Servers offering PSI-BLAST.

Site
SBASE 9.0 (Trieste)
NIH (Japan)
Pasteur Institute
CMBI, Netherlands
Human Genome Center, U. of Tokyo