[Bioperl-l] Local blast hit (hsp_hseq) extracted from fasta file

Hans-Rudolf Hotz hrh at fmi.ch
Thu Mar 10 17:37:07 UTC 2011

On 03/10/2011 06:13 PM, Ian Mc Dowell wrote:
> Hi all,
> I would like to take local blast hit sequences, i.e. hsp_hseq in blast xml
> format, and extract the full sequences of those hits from the original fasta
> file and put them in a fasta file of all hits that I can use later.
> This should be a widely performed task but I can't find any scripts that
> directly address this issue.  I have not acquired the skills to make my own
> scripts for this task.

Hi Ian

It is not a Bioperl solution, but a simple one:

Assuming, you are using the NCBI blast+ tools, make sure you create the 
BLAST indices with the "-parse_seqids" option. This will allow you to 
extract individual sequences (in fasta format) from the BLAST database 
with the command 'blastdbcmd' by providing a comma-delimited search 
string of sequence identifiers. Fore more details see:


Regards, Hans

> Thanks so much if you have anything that can help me out,
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
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