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Old 10-08-2013, 05:11 AM   #1
Location: haifa israel

Join Date: Jun 2011
Posts: 62
Default Best way to search for gene homologue in metagenomic dataset

Hi all,

This is my first foray into metagenomics so :

A collaborator has a metagenomic dataset (Illumina 100bpPE with ~200bp amplicons) and wants to search for her favorite gene in the dataset. So we are not looking for an exhaustive annotational but rather just want to fish out the Illumina reads that could be putative homologues of the gene.

(a) can I do this without assembling the metagenome?
(b) what is the best way? blast first or first fish putative ORFs from the raw Illumina data?

Happy for any recommendations!
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