How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?
2
0
Entering edit mode
5 weeks ago
mrj ▴ 70

I have performed blastx on a fasta file. I am trying to extract out the upstream region in fasta for all blastx hits.

I will be grateful to you if you can show me how to parse blastx output to get the final fasta file with only upstream regions.

fasta nr blastx upstream region • 947 views
ADD COMMENT
2
Entering edit mode
5 weeks ago

saving in outfmt6, converting to gtf/bed, and getting upstream sequences with bedtools or bedops.

ADD COMMENT
0
Entering edit mode

Thank you. This worked for me

ADD REPLY
1
Entering edit mode
5 weeks ago

You can use the blastdbcmd command to extract sequences (or ranges of it) directly from the blastDBs. Using the tabular blast output (as shenwei356 mentioned as well) will make this more easy.

ADD COMMENT
0
Entering edit mode

Thank you for your answer lieven.sterck

ADD REPLY

Login before adding your answer.

Traffic: 2779 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6