[Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA Sequences (reads)

shalabh sharma shalabh.sharma7 at gmail.com
Thu Mar 10 12:24:04 EST 2011


Hey Ian,
            I am not sure if i understood your problem completely.
But if you have ids of blast hits you can use 'fastacmd' to fetch sequences
from the database you used for blast.

-Shalabh Sharma
-----------------------------------------
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

On Thu, Mar 10, 2011 at 12:11 PM, Ian Mc Dowell <ian.mcdowell at gmail.com>wrote:

> Hi all,
>
> I would like to take local blast hit sequences, i.e. hsp_hseq, 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.
>
> Thanks so much if you have anything that can help me out,
>
> Ian McDowell
> Aquatic Pathology
> University of Rhode Island
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