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Psiblast Fasta Formatted Output

Hi,

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?

Thanks


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