GO Help query (from website)

[Pankaj Jaiswal]

Hi,

Using GO database tools is one way as described by Eurie Hong. You can 
do the same by visiting the BLAST services at Gramene database 
http://www.gramene.org/multi/blastview.
Paste the sequence and run either BLASTX against the Peptide (TIGR gene 
models) or BLASTN against the cDNAs (TIGR gene models). You will see 
that for AK110615 sequence the best match is on Chr-11 to the gene model 
LOC_Os11g14910.1
e.g a BLASTN query result is 	
http://www.gramene.org/Multi/blastview/BLA_TF8fLOMbn
Click on the name LOC_Os11g14910.1, it will take you to a gene report 
page where you will find GO annotations.

Another quick way to get this by avoiding BLAST is, try to search for 
AK110615 by visiting the marker database at Gramene 
(http://www.gramene.org/markers/index.html). Your search will result in
http://www.gramene.org/db/markers/marker_view?marker_name=AK110615
 From here if you go to the Map position tab (in green), where it says 
map position (3), you will see that it is mapped to Chr-11. Click on any 
of the genome browser position. On the genome browser you will see the 
mapped gene model and its details will take you to the same gene report 
as above for GO annotation.

We understand that it is a fairly long process to get to the information 
you would like to get without doing so much of querying. We are working 
towards minimizing the query effort.

Thanks
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