GO Help query (from website)

[Pankaj Jaiswal]

Hi Eurie,

Thanks for the help. I have replied the the person off the GO list with 
some more tips on querying the same at Gramene database.

BTW one aspect that I find from this query is that, more and more people 
want to know GO annotations using their source sequences from ESTs, GSS, 
cDNAs, UniGenes etc. Using the BLAST is a very effective way of doing 
this, but certainly not a good practice to ask everyone to perform 
BLAST. The solution, I see lies in mapping the  ESTs, GSS, cDNAs, 
UniGenes to the object we have in our Association files. This will give 
them a straight forward answer. I also agree that it is beyond the scope 
of GO, but is there a way the source dbs can provide the data (I am sure 
many of the have this kind of mapping), that can be used by GO to 
facilitate this query.

Pankaj

Eurie Hong wrote:
> Hello,
> 
> It appears that the cDNA clone with the GenBank accession AK110615 is 
> currently not annotated.   You can BLAST the sequence of AK110615 
> against the sequences available in AmiGO to identify if the gene that 
> encodes this cDNA has been annotated:
> 
> http://amigo.geneontology.org/cgi-bin/gost/gost.cgi
> 
> A BLASTX using the cDNA sequence hits the Oryza sativa (japonica 
> cultivar-group) gene Os11g0255500:
> 
> http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?search_constraint=gp&view=details&session_id=3361b1172551729&gp=Q53LC7 
> 
> 
> I am cc'ing the staff at Gramene (http://www.gramene.org/) who provide 
> GO annotations for Oryza sativa (japonica cultivar-group) so that they 
> can answer any further questions you might have.
> 
> Cheers,
> Eurie
> 
> *******************************************
> Eurie L. Hong, Ph.D.
> Scientific Curator
> Saccharomyces Genome Database: http://www.yeastgenome.org/
> Gene Ontology: http://www.geneontology.org/
> *******************************************
> 
> 
> On Feb 25, 2007, at 5:33 AM, noreply at genome.stanford.edu wrote:
> 
>> contactName: psrao
>> contactEmail: psrao at ccmb.res.in
>> contactText: Please ley me know how can I get GO terms(Go:7275) from 
>> NCBI Gene Accession numbers(AK110615)
>>
> 
> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683