blast results combining with genome annotation

Question

[Ric]

I have BLAST results and I just wondering what would be the easiest way to combine them with annotation in GFF3 files. I would like to get the gene name from the blast hit.

Thank you in advance.

Answer 1

[Prasad]

use intersectbed

[Ric]

I found blast2bed, but how can I can extract the intersect sequence?

[Prasad]

I thought you wanted gene name from the gff. What sequences you want to extract? Subject sequence to which your query is similar??

[Prasad]

fastaFromBed can be used to extract sequences

[Ric]

I found blast2bed, but how can I can extract the intersect sequence?