HELP

[Dave Matthews]

Hi Sofia,

Yes you're correct, these queries at http://wheat.pw.usda.gov/cgi-bin/gbrowse
don't work.  And this makes the site less useful than it might be.  We'll
think about how to improve that.

This site includes only a selected subset of the available data in order to
make the display not so huge it's impossible to read.  So the information
about both wheat ESTs and rice BACs is compressed.

For wheat ESTs, the only ones included are the contigs and singletons from an
assembly.  BE443401 isn't a singleton so you would have to search for the
contig it's in, contig-11915.1.  To find which contig an EST is in, a good
way is to go to http://wheat.pw.usda.gov/ITMI/WheatSNP/blastWheatSNP.html and
BLAST it against the default database, "Consensus sequences from Wheat SNP
Assembly, dec02".

For rice BACs, only a minimally overlapping set to cover the whole chromosome
is included and additional ones that would be redundant were removed.
AP004112 was removed.  I'm not sure if it would be possible to include all
the redundant ones without too much problem.  Jing, how many redundant ones
were there?  For now all I can suggest is to try some adjacent BACs.  In
this case contig-11915.1 is in the overlap of AP003370 and AP004357, and 
searching for either of those would find it.

I apologize for not being able to give you easier instructions.  The 
Generic Genome Browser is a wonderful tool but everything has limits and
we're still working on it.  Your question is good guidance for us.  Thank
you.

For a more inclusive search I recommend Gramene, www.gramene.org.  Searching
for BE443401 and AP004112 succeeds there.

best regards,
- Dave, GrainGenes curator


> Date: Sun, 15 Jun 2003 17:52:20 -0500 (CDT)
> From: =?iso-8859-1?q?Sof=EDa=20Olmos?= <se_olmos at yahoo.com>
> Subject: HELP
> To: curator at pw.usda.gov
> 
>  Hi my dear Curator,
> I would greatly appreciate if you can help to use the Generic Genome Browser
> for wheat-rice comparative mapping using the Rice chromosome 1 vs. cereal
> genes we site:
> 
> When I enter an accession number from the GenBank (let say
> gi|9442934|gb|BE443401.1|[9442934]) the program tell me this landmark doesnt
> exist.
> 
> On the other side, when I look for a BAC (let say, accession AP004112 from
> the TIGR (Oryza sativa spp japonica cv. Nipponbare) proyect, I have the same
> result than above.
> 
> Thank you so and so much,
> Sofia