Table 2. Similarity Search Programs and Servers
Different Types of BLAST (Basic Local Alignment Search Tool)
Program Query Database Comparison Usage
BLASTN DNA DNA DNA Level Identify very similar sequences; seek splicing patterns or non-coding DNA
BLASTP Protein Protein Protein Level Find homologous proteins (>40% identity)
BLASTX DNA Protein Protein Level Analyze new DNA to find genes and homologous proteins
TBLASTN Protein DNA Protein Level Search for genes in unannotated DNA
TBLASTX DNA DNA Protein Level Protein discovery. EST discovery
PSI-BLAST Protein Protein Protein Level Detects remote similarity (>20%) and finds divergent family members
Major Online Servers for Similarity Searches
Location Program Website
USA BLAST http://www.genome.wustl.edu/tools/blast/
USA BLAST http://www.pir.uniprot.org/search/blast.shtml
Europe BLAST http://www.ch.embnet.org/software/bBLAST.html
Europe BLAST http://www.ebi.ac.uk/blast/index.shtml
Europe BLAST http://www.expasy.org/tools/blast/
Europe BLAST/PSI-BLAST http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.shtml
USA BLAST/PSI-BLAST http://www.ncbi.nih.gov/BLAST/
Japan BLAST/PSI-BLAST http://www.ddbj.nig.ac.jp/search/psi_blast-e.html
USA FASTA http://vigen.biochem.vt.edu/vigenblast.php
Europe FASTA http://www.ebi.ac.uk/fasta/index.html
Europe SSEARCH http://www.ch.embnet.org/software/GMFDF_form.html
Europe SSEARCH/FASTA http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_server.html
Japan SSEARCH/FASTA http://www.ddbj.nig.ac.jp/search/Welcome.html
Search Against Your Own Sequence Database
Location Website Usage
Proweb.org http://proweb.org/Tools/WU-blast.html Customize a BLAST database for similarity searches (Protein or DNA)