Gene Ontology Term Generation For Keywords

Question

[Raghul]

Hi to all, I have found the most probable function for sequences using HMM methods. These sequences do not have database hits when using blastx or blastp. So, now I want to get Gene ontology terms for around 2000 sequences that has been annotated by HMM methods. There are keywords like ABC transporter, ribosomal protein,acetyltransferase etc. So I want to generate the 3 GO category maps for these sequences just like blast2go. This could give some idea what these species-specific genes could code for?

Is it possible to do in this case when there is no GO id or gene id etc ?

I use hhblits searching Uniprot database but "HHblits database is a clustered version in which each set of full-length alignable sequences is represented by an HMM"

The output has a keyword "BOZFAWOB,PIXMOMOBA" but I am not sure whether it could be helpful Here is a part of result

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM

1 UP20|BOZFAWOBA|1|90 Putative u 88.6 0.33 2.7E-06 38.2 0.0 42 48-89 11-52 (90)

2 UP20|PIXMOMOBA|1|127 Putative 87.6 0.44 3.5E-06 39.3 0.0 34 24-58 51-88 (127)

Thank you raghul

Answer 1

[Damian Kao]

What HMM databases did you use for the annotation? There are GO indices available that maps several HMM databases (pfam,prosite,smart...) to GO terms. Check here: http://www.geneontology.org/GO.indices.shtml

[Raghul]

There are Uniprot IDs in my output file,QuickGO gives info for these IDs one at a time. Is there any tool available to do this for large number of IDs? thanks

[Damian Kao]

Here is a link to the gene association files for uniprot: http://www.ebi.ac.uk/GOA/downloads.html