[Bioperl-l] From Blast hits to Taxanomy lineage for Short DNA Sequences (reads)
miguel.pignatelli at uv.es
Wed Mar 9 04:20:47 EST 2011
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
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 ->
> I want to get the lineage for this specie.
> The final goal is to do the above mapping as efficiently as possible.
> Any pointers will be appreciated.
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> Bioperl-l at lists.open-bio.org
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