When I do PSI-BLAST for a protein sequence against a non-redundant database (3 iterations) I get a PSSM matrix. Is it possible to generate any other output from PSI-BLAST for the above problem which is in a form of 8D output vector? I need to know the result of the similarity match of the given protein sequence against NR database using PSI-BLAST.
Are you using standalone BLAST?? It can be downloaded from the NCBI website and used on the command line. You then have much more control over output format (and other things). For example you can generate a comma separated value output file with whichever fields you choose. This makes it easy to parse the data (with perl or something similar) into any format you can dream up.
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Hope this helps.....
No I am using standalone PSI-BLAST and I am getting PSSM fille on 3 iterations. But in some paper I have read that they have generated an 8dimensional output vector from PSI-BLAST which I did not understand how. With standalone blast I am comfortable.
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