PSI-BLAST (SOAP) SOAP

Position Specific Iterative BLAST (PSI-BLAST) refers to a feature of NCBI BLAST 2.0 in which a position-specific scoring matrix (PSSM) profile is constructed from set of BLAST alignments. The PSSM is then used to search the database in subsequent iterations allowing the detection of distant evolutionary relationships. This can be combined with the Pattern Hit Initiated BLAST (PHI-BLAST) mode to constrain the PSSM using a ProSite pattern to define the region(s) to be used when building the PSSM.

Position Specific Iterative BLAST (PSI-BLAST) refers to a feature of NCBI BLAST 2.0 in which a position-specific scoring matrix (PSSM) profile is constructed from set of BLAST alignments.

Free.

E-mail supplied for submission must be a valid e-mail address and no more than 25 concurrent jobs should be submitted at any one time, see http://www.ebi.ac.uk/Tools/webservices/about/webservices and the EMBL-EBI Terms of Use: http://www.ebi.ac.uk/Information/termsofuse.html

http://www.ebi.ac.uk/support/

Goujon M., McWilliam H., Li W., Valentin F., Squizzato S., Paern J. and Lopez R. (2010) “A new bioinformatics analysis tools framework at EMBL-EBI.” Nucleic Acids Res. 38:W695-9 PMID: 20439314 (http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=20439314&dataSource=MED) DOI: 10.1093/nar/gkq313 (http://dx.doi.org/10.1093/nar/gkq313)

Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res. 25(17):3389-402. PMID: 9254694 (http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=9254694&dataSource=MED) DOI: 10.1093/nar/25.17.3389 (http://dx.doi.org/10.1093/nar/25.17.3389)