[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,


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,



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