You may use the Protein Ontology tool at PIR http://pir.georgetown.edu/pirwww/search/fasta.shtml

Hi Sandeep

I think OBO-Edit tool will help you. It is an open source, platform-independent application for viewing and editing ontologies. You may reach the homepage at

http://www.oboedit.org/

interproscan

Hi

first, convert your fasta sequence to know the protein

or do you know the name of the protein?

here you can enter your sequence http://amigo.geneontology.org/cgi-bin/amigo/blast.cgi?session_id=

and then, enter the accesion number y go, to obtain the Go annotation

Does blast2Go not handle protein FASTA? Pretty sure I've done it with amino acid sequences.

Thank you all of you. Actually I was out of the lab for 2 days. and Joseph blast2Go handles FASTA amino input, but I am in search of free tool as in my query, but its free upto 7 days trail.

As far as I remember, the primary functions of BLAST2GO are free, indefinitely. While upgrading to the "Pro" version provides some added conveniences, you should be able to BLAST, map, and annotate your sequences without paying anything. Perhaps it is the "Pro" version that is a seven day trial.

Seeing as you already know the protein sequence you can search (via blast) for it at www.uniprot.org which give you all the information you need for your protein

hi dear,

i recommend you I-Tasser and interproscan which give you comprehensive results of GO with respect to function based structural homology of your pdb sequences. be happy