Database search
Sequence similarity search against DNA or protein sequence database is
one of the most extensive used approaches in the application of bioinformatics
to molecular biology and genome research. Results of database search can
deduce biological function for the newly identified sequence or to infer
evolutionarily relationship among the query sequence and a group of matched
subject sequences. The most famous program for database search is BLAST
- the Basic Local Alignment Search Tool. Thanks to the BLAST team at NCBI
who keep continuously development of this package and make it freely available
for the community. Here, we introduce several BLAST web servers which are
mostly accessed, as well as the FASTA, BLAT and MPSearch servers.
BLAST search
- NCBI BLAST
- The central point of the NCBI BLAST server which provides whole functionality
of DNA and protein sequence database search programs including PSI-BLAST
and PHI-BLAST, and the whole list of databases in different scales and
different genomes.
- EBI BLAST - The entry page
of the EBI BLAST facility which provides both NCBI-BLAST and WU-BLAST
programs, as well a set of specialized BLAST programs to search the alternative
splicing database, the cloning vector database, and the parasite database.
- WU-BLAST - The entry page of
the WU-BLAST maintained by Warren Gish at Washington University. It provides
several links to other BLAST servers world wide.
- Sanger BLAST
- The entry
page of the sequence projects BLAST search services at the Sanger Institute,
featured with the special genome databases generated by the completed
or ongoing sequencing projects.
Other database search
- FASTA
- The original web site for the FASTA set programs maintained by William
Pearson at the University of Virginia. It provides extensive documents
and help materials as well.
- EBI FASTA - The entry page
of EBI FASTA services. FASTA has a higher sensitivity in some cases comparing
with BLAST with a slightly lower speed. It is specific to identify low
similarity long regions for highly diverged sequences.
- MPSrch - The EBI MPSrch
server which uses the Smith-Waterman algorithm to obtain the optimal sequence
alignment results.
- GoldenPath BLAT
- The web server for the genome database search, integrated in the GoldenPath
platform.
- ENSEMBL BLAT -
The web server for the genome database search, integrated in the ENSEMBL
platform.
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| 16 July 2008, J Luo, CBI, PKU, Beijing, China