Functionnal annotation of metagenomes
Hi everyone,
I'm currently starting in metagenomics and I would like to compare the overall functions present in different samples (I already have the sequences of the ORFs). Which method do you recommend for that ?
I came across Fun4me that looks like what I am looking for but nobody seems to use that. Several people said I should use the results from blast again nr or RefSeq but I don't see how to make the link between the gene description and functions present in a large sample. I think I need to find a way to directly target protein functions and visualize it (for example via the GO term). Any suggestions ?
Thanks very much !!
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Hi :)
Fun4me is a new package, that uses several other well-used tools. For instance,
Fraggenescan(bacterial gene prediction), has been cited 559 time,RAPSearch2(protein similarity search), 332 time ,Minpath(metabolic pathway reconstruction) 218 times. Fun4me also performs similarity search against GO (Gene Ontology) and EC (Enzyme Commission).