How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?

Question

[mrj]

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.

Answer 1

[shenwei356]

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

[mrj]

Thank you. This worked for me

Answer 2

[lieven.sterck]

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.

[mrj]

Thank you for your answer lieven.sterck