I have a FASTA formatted protein sequence (stored in DsbA.fa) and I would like to use PSI-BLAST (not the web server. The command line in the BLAST+ package) to generate hits. I am using the following command line:
./psiblast -query DsbA.fa -db Proteobacteria -num_iterations=6 -evalue=0.005 -out psiblastDsbAOut -out_pssm=PSSMDsbA
My problem is that I would like a FASTA formatted out put of my result (psiblastDsbAOut) so I can re-align the hits using Clustal.
The output formats supported by psiblast are:
*** Formatting options -outfmt <String> alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1, 10 = Comma-separated values, 11 = BLAST archive format (ASN.1) Options 6, 7, and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers.
Do you know if I can make the output in FASTA format? if not is Clustal happy to take any of these formats as input?