Extract sequences from the blast results

Question

[vmevada102]

After Performing Local Blast against NT database results generated into the *.blast files.

Now i would like to extract the sequences which are aligned and from my original sequences present into input *.fasta file.

I have tried the tool faSomeRecords.py which extracts the results. But the problem is to create the list of sequences

python faSomeRecords.py -f candidate.list -o candidate_sequences.fasta

In other way, if we can create the list of seqeunces from *.blast sequences. Then faSomeRecords.py will extracts the sequences for us.

[iraun]

Have you tried the solutions suggested here: How to retrieve fasta sequence after local blast? ?

[GenoMax]

But the problem is to create the list of sequences

It would be best to have the blast results in columnar output format (like 6) to be able to easily extract the hit ID's. If you have results in html or some other format then parsing them would be more difficult.

Once you get that list using blastdbcmd is the easiest option to retrieve sequences from a local blast database.