sequence tally?

[archak at cdfd.org.in]

Hi,

Thanks for the mail. 
I was searching for the homologies in the rice genome for the following 
aa sequence: ARECETESSKFSGMCMIQANCDHICMGGDDCRGFRRRCMCRTQC 

After running tblastn available at Gramene site in IRGSP rice genome japonica 
database, one of the matches was: 
1143309 ARECETESSKFSGMCMIQANCDHICMG----GDDCRGFRRRCMCRTQC 1143178
on chromosome 4.3.

When I tried to locate the same positions on “rice genome view” at Gramene 
site (http://www.gramene.org/japonica/contigview?chr=4&vc_start=6400000) 
“jump to” option, I was led to Chr 4.1. 

Am I folowing the correct procedure? What might be wrong?

Sincerely,

Sunil Archak
PhD Student
Laboratory of Molecular Genetics
CDFD
Nacharam,
Hyderabad-500 076, INDIA.
Tel : +91-40-27151344  extn: 1102
Fax : +91-40-27155610  

---------REPLY TO-------------
Date:Wed Oct 01 00:41:11 CST 2003
FROM: Steven Schmidt  <schmidt at cshl.edu>
To: gramene at gramene.org, archak at cdfd.org.in
Subject: Re: sequence tally?
Hi,

Perhaps we have gone wrong.
What is the sequence?

-Steve

On Friday 26 September 2003 17:07, archak at cdfd.org.in wrote:
> Hi,
>
> I ran blast for a particular peptide sequence a got few matches in
> the rice genome along with the positions. However, when I went to
> those positions on the contig view, I could not find the same(among
> six frame aa sequences). Where have I gone wrong?
>
> Sunil Archak
> PhD Student
> Laboratory of Molecular Genetics
> CDFD
> Nacharam,
> Hyderabad-500 076, INDIA.
> Tel : +91-40-27151344  extn: 1102
> Fax : +91-40-27155610
>
> -

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-8892



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