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
Publication Details
Publication History
Created: June 23, 2008; Last Update: January 7, 2021.
Copyright
BLAST is a Registered Trademark of the National Library of Medicine
Publisher
National Center for Biotechnology Information (US), Bethesda (MD)
NLM Citation
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. 2008 Jun 23 [Updated 2021 Jan 7].