PSI-BLAST help

A brief introduction to PSI-BLAST
The BLAST algorithm could use a position-specific matrix (profile) in place of a query sequence and associated substitution matrix. The PSI-BLAST (Position-Specific Iterated BLAST) is an automated procedure generating the matrix from BLAST result and a modified BLAST algorithm to take as input this matrix. The PSI-BLAST is an iterative process with a first step being a standard BLAST.
For further details, see the NCBI PSI-BLAST tutorial.

Availability in NPS@
PSI-BLAST is available :

So, for example, you can use PSI-BLAST to find similar sequences in a database built from an ACNUC query or after a PATTINPROT search.

Parameters
PSI-BLAST parameters are not currently available for the user.
By default the number of description and the number of alignment are set to 500.
The expected threshold is set to 10.0.
The comparison matrix is BLOSUM62.
The default behavior is selected for gap opening (11) and gap extending (1) costs.
The expectation value threshold for inclusion in multipass model is 0.01.
The maximum number of passes is 10.
To retrieve these informations see the line "Information and statistics : [PSI-BLAST]" in NPS@ PSI-BLAST result file.

NPS@ PSI-BLAST output example
The NPS@ PSI-BLAST output is divided into three parts.

References


User : public@35.170.81.210. Last modification time : Thu Jan 14 19:03:12 2016. Current time : Fri Dec 6 19:14:02 2019