Blastp command line to get only full matches of query sequence

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7.0 years ago

rlee03 • 0

Hi, I have a downloaded blast database already. Is it possible to blast this database and only get all the sequences in the database that contain EXACTLY this sequence ADARS ?

In other words, if any protein sequence contains ADARS EXACTLY, then I would you in my XML output/, this is my code so far. Thanks.

blastp -outfmt 5 -query /usr/local/projects/heptamer/peptide.fa -word_size 2 -matrix=PAM30 -db /usr/local/projects/heptamer/blastDB/specialBlastDB/BacteriaNR/all_bacteria_nonredundant_protein.faa -out /usr/local/projects/heptamer/blastResults/blastp/Bacteria/BacteriaFTP.xml -evalue 1000000000000000000000000000 -max_target_seqs 5000000

blast blastp commandline exact • 2.7k views

ADD COMMENT • link 7.0 years ago by rlee03 • 0

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Have you looked at the qcovs parameter?

ADD REPLY • link 7.0 years ago by GenoMax 141k

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What about grep -B 1 ADARS all_bacteria_nonredundant_protein.fa or variants thereof ?

ADD REPLY • link 7.0 years ago by Jean-Karim Heriche 27k

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This assumes unformatted fasta, though.

ADD REPLY • link 7.0 years ago by cschu181 ★ 2.8k

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Yes, the rest is covered in the 'variants' part :)

ADD REPLY • link 7.0 years ago by Jean-Karim Heriche 27k

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Thank you all for your help. The qcov worked!

ADD REPLY • link 7.0 years ago by rlee03 • 0

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