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

Abhishek Pratap abhishek.vit at gmail.com
Tue Mar 8 17:42:03 EST 2011


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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