Is There any command for retrieval (extraction) of covered sequence using Linux (offlineBLAST)

Question

[armaansiraj2]

Is There any command for retrieval (extraction) of covered sequence using Linux (offlineBLAST)? Im in trouble since one week, if someone here and understand please share and specify. Thanks

[cpad0112]

if you can post example input and expected output, some one here may help.

Answer 1

[Mensur Dlakic]

Not completely clear what you want, but maybe this will work. A part of comer package is blast2fa.pl script.

https://github.com/minmarg/comer2/blob/master/Linux_installer/bin/blast2fa.pl

[armaansiraj2]

Sir I mean that I ran BLAST between two sequences. And the results came what I want, but I need now the "region" covered within target sequence in FASTA format. And for that purpose I need a command to extract the covered region. Hope u get the point.

Answer 2

[lieven.sterck]

not sure if there will exists an off the shelf solution for this.

One thing you might be able to do is to get the tabular output, and customise that one by adding the field to include the aligned region,. Afterwards you can select that column from the output and format it as fasta.