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BLAST® Command Line Applications User Manual [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-.

Specifying a sequence as the multiple sequence alignment master in psiblast

Created: ; Last Update: January 7, 2021.

The -in_msa psiblast option, unlike blastpgp, does not support the specification of a master sequence via the -query option, so if one wants to specify a sequence (other than the first one) in the multiple sequence alignment file to be the master sequence, this has to be specified via the -msa_master_idx option. For instance, in the example below, the third sequence in the multiple sequence alignment would be used as the master sequence:

psiblast -in_msa align1 -db pataa -msa_master_idx 3
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