Functionnal annotation of metagenomes

0

Entering edit mode

5.3 years ago

lagartija ▴ 160

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 !!

metagenomics protein function • 823 views

ADD COMMENT • link 5.3 years ago by lagartija ▴ 160

1

Entering edit mode

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).

ADD REPLY • link 3.5 years ago by Fatima ▴ 1000

Login before adding your answer.