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