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

Abhishek Pratap 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.

Best,
-Abhi

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.
> 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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>>>
>>
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