Functional annotations in metagenomics

Question

[int11ap1]

Hi everybody,

I am designing a novel pipeline for processing metagenomic datasets. I'd like to use for functional annotation the following methods:

1) Full domain alignment methods (e.g. Pfam and TIGRFam)
2) Multiple motif methods (PRINTS)
3) Single motif methods (ProSite)

I guess that this list goes from very specific methods (1-->Pfam) to very sensitive methods (3-->ProSite), right? Thus, do you recommend me to analyse my sequences with Pfam first, then to analyse the remaining unannotated sequences with PRINTS and finishing with ProSite?

I cannot see the differences between Pfam and TIGRFam.

Any suggestion?
Thanks!

Answer 1

[cdsouthan]

Just run the InterPro pipe/engine http://www.ebi.ac.uk/interpro/. You get all these methods rolled in. Better still you could ask the EBI nicely to do it for you https://www.ebi.ac.uk/metagenomics/info and orientate your project more towards the comparative analysis end

[int11ap1]

If I run InterProScan, the output will be something like this:

P51587  14086411a2cdf1c4cba63020e1622579        3418    Pfam    PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1        2670    2799    7.9E-43 T       15-03-2013
P51587  14086411a2cdf1c4cba63020e1622579        3418    ProSiteProfiles PS50138 BRCA2 repeat profile.   1002    1036    0.0     T       18-03-2013      IPR002093       BRCA2 repeat    GO:0005515|GO:0006302
P51587  14086411a2cdf1c4cba63020e1622579        3418    Gene3D  G3DSA:2.40.50.140               2966    3051    3.1E-52 T       15-03-2013

I can have this results using the three approaches I posted (which are used by InterProScan as well). However, your answer does not answer my question. I wanna do a fast pipeline, where annotated sequences are not subsequently reanalysed by the following steps (this does not happen in InterProScan). For this, I must set an order. The main aim is to get GOs.

[cdsouthan]

InterPro to GO? http://www.ebi.ac.uk/GOA/InterPro2GO