Question: Blastp command line to get only full matches of query sequence
0
gravatar for rlee03
2.0 years ago by
rlee030
United States
rlee030 wrote:

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

exact blastp blast commandline • 1.1k views
ADD COMMENTlink written 2.0 years ago by rlee030

Have you looked at the qcovs parameter?

ADD REPLYlink written 2.0 years ago by genomax65k

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

ADD REPLYlink written 2.0 years ago by Jean-Karim Heriche18k

This assumes unformatted fasta, though.

ADD REPLYlink written 2.0 years ago by cschu1811.6k

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

ADD REPLYlink written 2.0 years ago by Jean-Karim Heriche18k

Thank you all for your help. The qcov worked!

ADD REPLYlink written 2.0 years ago by rlee030
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