[Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA Sequences (reads)
abhishek.vit at gmail.com
Wed Mar 9 22:25:58 EST 2011
Thanks guys. I could not try either method today but will get back to
you if I face problem.
On Wed, Mar 9, 2011 at 9:34 AM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hey Abhishek:
> The other way to deal with this that you can download
> the gi_taxaid file from ncbi.
> Convert all your GI's to taxaid and use Bio::DB:Taxanomy.
> I think there are lot of other options too, if you are interested you can
> search for the thread which i started long time back.
> Hope this helps.
> -Shalabh Sharma
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> On Wed, Mar 9, 2011 at 4:20 AM, Miguel Pignatelli <miguel.pignatelli at uv.es>
>> Hi Abhishek,
>> For a non bioperl related solution, take a look at Bio::LITE::Taxonomy.
>> It has been design to deal with great number of sequences (it is fast and
>> You may also find interesting the Blast2lca tool,
>> It currently works with the best hits for each query (calculates the lower
>> common ancestor), but if you want to use only the best hit, please drop me a
>> Please, let me know if you need further help with any of these,
>> On 08/03/11 22:42, Abhishek Pratap wrote:
>>> Hi All
>>> I have results from different megablast of short reads(DNA sequences)
>>> and after extracting the tophit for each read I want to bin them by
>>> their lineage creating a tree.
>>> For example.
>>> If blast query hits the reference ->
>>> I want to get the lineage for this specie.
>>> The final goal is to do the above mapping as efficiently as possible.
>>> Any pointers will be appreciated.
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
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