Best way to search for gene homologue in metagenomic dataset

[Noa]

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!

[rhinoceros]

I'm confused. Your question implies that you have a WGS metagenome but then you use the word amplicon. Anyway, maybe you could do a reference guided assembly using your favorite gene as a reference? Alternative you could map your reads against a representative set of your favorite gene and then assemble those reads? There are so many ways to do this..

[Noa]

Sorry for the confusion!
We have a WGS metagenome; ignore the word amplicon here. I think they somehow tried to select for short fragments when the prepared the library but I will double check on this. (ie, not sure whether this means the 100bp PE is overlapping or no). Like I said- new to metagenomes....

Any suggestions as to the best programs to use for ref-guided assembly? Although I have about 50 homologues of the gene and I am not really sure which to choose.

Thanks for your advice!