Hi,

My question is how to do a GO analysis with 'genes' using bioconductor
tools.




On Fri, Jan 31, 2014 at 10:04 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> 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
>

	[[alternative HTML version deleted]]

