[BioC] Ontology

[Steve Lianoglou]

Hi,

Please use reply-all to keep conversations on the bioc-list, that way 
you can get better help and others can also use it as a resource.

That having been said:

On 31 Jan 2014, at 10:48, Orcun Hacariz wrote:

> Hi,
>
> These are the assembled sequences that were obtained from a sequencing
> experiment.  The sequences were annotated against different databases 
> using
> the blast programme. Basically, each sequence is matching a protein or
> nucleotide in the public databases. But, I also want to annotate these
> sequences based on their biological function (such as molecular 
> function).
> For example, a sequence is matching with Cathepsin L1 protein. I know 
> this.
> But, I want to get the software blast this sequence against an 
> ontology
> database and report the biological function(s) of this protein (it 
> should
> report that this protein is associated with proteolitic activity, for 
> this
> example).

I think I'm still missing something.

You've used BLAST to associate the sequence to a particular gene. Now, 
once you have the sequence <--> gene mapping, doing GO ontology stuff on 
the gene list is rather straightforward.

So, is your question how to do a GO analysis with *genes* using 
bioconductor tools? Or do you want to have a Bioconductor tool that you 
can feed sequences to and have it match the organism and gene that it's 
coming from?

Or ... ?

-steve

--
Steve Lianoglou
Computational Biologist
Genentech