[Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA Sequences (reads)
shalabh.sharma7 at gmail.com
Thu Mar 10 17:24:04 UTC 2011
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.
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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