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

shalabh sharma shalabh.sharma7 at gmail.com
Wed Mar 9 12:34:57 EST 2011


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.
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Taxon.html

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>wrote:

> 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
> efficient).
>
> You may also find interesting the Blast2lca tool,
>
> https://github.com/emepyc/Blast2lca
>
> 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
> line.
>
> Please, let me know if you need further help with any of these,
>
> Cheers,
>
> M;
>
>
>
>
> 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 ->
>>
>> gi|196110604|gb|CP001103.1|__Alteromonas_macleodii_'Deep_ecotype',_complete_genome
>>
>> I want to get the lineage for this specie.
>>
>>
>> Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Alteromonas;Alteromona
>>
>> The final goal is to do the above mapping as efficiently as possible.
>> Any pointers will be appreciated.
>>
>>
>> Thanks!
>> -Abhi
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