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

Ian Mc Dowell ian.mcdowell at gmail.com
Thu Mar 10 12:31:29 EST 2011


I have a deeply sequenced transcriptome so when I look for a gene of
interest in my short reads (108bp) I get thousands of hits, at very low E
values.  And I want to do this for many sequences of interest. That's why I
want a script to automate the process of grabbing the accession numbers from
the blast xml output, then searching in the fasta file which is equivalent
to my local database and pulling those relevant reads.

On Thu, Mar 10, 2011 at 12:24 PM, shalabh sharma
<shalabh.sharma7 at gmail.com>wrote:

> 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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>
>


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