[BioC] gene function assessment

[Abhishek Pratap]

Hi Sean

I see. I was wondering if I can scan my sequences against InterPro
(EBI) and get the GO information from there. Any package in
bioconductor or may be I need to use their API.

Thanks!
-Abhi

On Fri, Feb 10, 2012 at 6:10 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Fri, Feb 10, 2012 at 7:48 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
>> Unfortunately the gene id's are local to us.  So there will be no
>> mapping between them to RefSeq, Entrez etc.
>
> Assuming that you mean that you do not have GenBank or any other
> public ID, I see no option for you except to start BLASTing to get
> some useful ID.
>
> Sean
>
>
>> On Fri, Feb 10, 2012 at 4:45 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>> On Fri, Feb 10, 2012 at 3:50 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
>>>> Chlamydomonas.  I was reading a bit more about this ..so I guess what I
>>>> might need to do is associate GO ID for each gene in my set and the may be
>>>> use GOSeq like packages but I am not sure how should I go about associating
>>>> GO ID's to genes.
>>>
>>> And what, exactly, are your gene ids?  Are they Entrez Gene IDs,
>>> RefSeq, Genbank, or something else?
>>>
>>>> On Fri, Feb 10, 2012 at 12:46 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>>>
>>>>> What organism?
>>>>>
>>>>> On Fri, Feb 10, 2012 at 2:48 PM, Abhishek Pratap <apratap at lbl.gov> wrote:
>>>>> > We have identified a set of genes to be differentially expressed between
>>>>> > treatment and control.  The current gene annotation doesnt have
>>>>> functional
>>>>> > information about the gene.
>>>>> >
>>>>> > What we would like to do is asses the biological functions of these
>>>>> genes(
>>>>> > may be based on GO and then cluster them). I was wondering if there is
>>>>> > something already out there to do so in semi automated way.
>>>>> >
>>>>> > I am thinking of blasting them against pfam  or be myhits dbase but
>>>>> wanted
>>>>> > to take your opinion.
>>>>> >
>>>>> > PS  : cross posted on biostar mailing list :
>>>>> >
>>>>> http://biostar.stackexchange.com/questions/17332/functional-assessment-of-genes
>>>>> >
>>>>> > Thanks!
>>>>> > -Abhi
>>>>> >
>>>>> >        [[alternative HTML version deleted]]
>>>>> >
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>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
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