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How Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?

help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in blast program, im using blast 2.2.27+, i have used makeblastdb command.

pssm blast
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updated by Hamish Hamish • written by bhavanireddy04 • bhavanireddy04

What have you tried so far? Have you read the BLAST+ documentation?

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written by Neilfws Neilfws

1 answer

To search a nucleotide database with a PSSM using NCBI BLAST you will want to use PSI-tblastn. See:

Please note that PSI-tblastn is not recommend in cases where a suitable protein database for use with PSI-BLAST is available. Assuming that you are interested in a specific organism or organisms proteomes you should check to see if completed proteomes exist for your species of interest (see http://www.uniprot.org/taxonomy/complete-proteomes), and use those with PSI-BLAST if appropriate.

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written by Hamish Hamish

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