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

Miguel Pignatelli miguel.pignatelli at uv.es
Wed Mar 9 04:20:47 EST 2011


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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



More information about the Bioperl-l mailing list