How can I get do this?

[SDPA_Pet]

Hey, I am working on some metagenomic data. I blast my pyrosequencing reads against some protein databases (e.g., COG, KEGG) to get the functional information. This results will show the number of reads assigned to each function.

However, I would like to know the the taxonomic information associated with each functions. For example, I find 10 reads assigned to COG001, I would like to know what organisms they are.

I am not sure how can I get the functional information and taxonomic information at the same time.

The methods that I could think is to blast twice. First, blast against protein database. Second, extract the functions that I'm interested in (e.g, nitrogen functions) and blast again to find taxonomic information. However, sometime when I get the functional information from blast, it only shows the number of reads instead of which reads.

Anyone can recommend software can give functional and taxonomic info at same time.

[maubp]

I suggest NCBI BLAST+ with its tabular output which can include the taxonomy information if present in the BLAST database you are using (this should work the NR database). See:

http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html

[SDPA_Pet]

Hi maubp,

Yes, I could do the blast against NR database, but it won't give you functional information. I want this kind of information. For example, use RPS-BLAST against NCBI COG database or HMMM against pfam, KEGG database.

[Zapages]

You could try the following:

BLASTX NR or specific database of interest > Output XML > BLAST2GO and Interproscan. This will provide you some functionality information as well.

[SDPA_Pet]

Hi Zapages,

Thanks, I need to pay to use BLAST2GO for large datasets,right?

[Zapages]

Hi Zapages,

Thanks, I need to pay to use BLAST2GO for large datasets,right?

If you can run a local BLASTX and then use GO portion of BLAST2GO, which is free.

[SDPA_Pet]

If you can run a local BLASTX and then use GO portion of BLAST2GO, which is free.

Thanks you.

[SDPA_Pet]

If you can run a local BLASTX and then use GO portion of BLAST2GO, which is free.

Hi, do you mean I run the online Java based version of BLAST2Go or I need to install it on local computer?

[Zapages]

I don't think it is feasible to run BLASTx on a normal computer. The best method would be install BLAST+ which includes BLASTx, BLASTn, BLASTp, etc on workstation/server.

Also download the NR database from NCBI on the workstation/server. Its nice that it can update itself when there are new update for NR.

Have the output be XML from BLAST+. Then from there import into the Java version of BLAST2GO. Then run the GO portion of BLAST2GO.

I hope this helps a bit. If this is not feasible, let me know there other alternative paths you may take.

[SDPA_Pet]

OK. Yes, I finished blast using super computer. What I asked is the GO part. So, the go part has to be run on java platform? I can't install it locally right?

I'm running with the GO part right now with my laptop. It seems I have to connect it with their server. I can't turn off my computer or pause my job.