From kumark at cshl.edu  Wed Sep  1 10:05:28 2004
From: kumark at cshl.edu (Kiran Kumar)
Date: Wed, 1 Sep 2004 10:05:28 -0400 (EDT)
Subject: Blastn against Rice_genome_japonica_TIGR
In-Reply-To: <718239D42CCAD611B3D700C04F070557A1850C@ICRSATY>
Message-ID: <Pine.GSO.4.05.10409010959350.1240-100000@phage.cshl.edu>


Hi Ramu,
It works for us over here. I pasted the sequence below at
http://www.gramene.org/db/searches/blast and RunBlast and it gives the
following results header followed by a detailed alignment.

chr1 : 2997635-2998018  	Alignment 	466 	8.1e-15 	1

1 hits total (1 shown)


I am guessing it could be problem with your browser. It somehow is not
able to send the sequence to the gramene_blast. Please try again and let
us know and we shall try to investigate further.

Regards,
Kiran





On Mon, 30 Aug 2004, Punna, Ramu (ICRISAT- IN) wrote:

>Dear Sir/Madam,
>
>I,Punna Ramu, working as research scholor in ICRISAT. I'm doing blast search
>of Sorghum sequences against Rice_genome_japonica_TIGR. The blastn results
>saying that it is not able to read the blast sequence. We are not able to
>find the problem from last three days. We dont know whether the problem in
>site or with us. We are giving it in Fasta Format. Can you help in this
>aspect to get the results?
>
>I'm sending you a sample of sequence.
>
>>AW679289
>TACGGCGGCCATGGGCATGGATACGGCGGCCATGGGCAGGGCTACGGCCACGCGTACCCTCCTCCGGCCGCCGCCG
>GCGCGTACCCTCCTCCGCGCACTCGGCGCACTACGGGAACATGGGATCGTACCACAGCAGCCACAGCCATGGCGGC
>GGCCACCACGGCGGCTACGGCGGCAAGCACAAGGGCGGCATGTTCGGCGGCGGCAAGTTCAGGAAGTGGAAGTGAA
>GCTGAAAGCCATCGATCGAAACTACGTATCTGCCAGCCGGCAGCCGCGTACGTACGTACGTACGTATCCTGCCAGC
>CGTAGCTAAGCATGCACTGCACACAGTTCCTATAAATAAATTAAATAAAGTAGTGCAAGCAGGCAGGACGCGTCCT
>ACGTGTATCGTTATTTGTATACGGAATAAAGTGAGACGTGTGTTTCTGGTCATGTTCATGTAACGTGCTCGGCGTA
>TGTACCACCATGCATGCAGTGTTGTATACCAGTCGTATATACAGTACAAGCCGAGTATAACCTG
>
>Thanking you sir/Madam,
>
>I look forward for your mail.
>
>Ramu.P
>



From r.punna at cgiar.org  Tue Sep  7 23:55:15 2004
From: r.punna at cgiar.org (Punna, Ramu (ICRISAT- IN))
Date: Tue, 07 Sep 2004 20:55:15 -0700
Subject: Gramene Blast Search
Message-ID: <718239D42CCAD611B3D700C04F070557A317D5@ICRSATY>

Dear Sir,

Gramene blast is not working regularly.
When we blast the sequences sometimes it is showing 'blank page' again or
showing 'page cannot be displayed'. Everyday we are not able to blast more
than 30-50.
Remaining things in Gramene are working very fine.

Please find if there is any problem.

I look forward for your mail.

With best regards,

Ramu.P
Research Scholar
ICRISAT, Patancheru,
India.


From kumark at cshl.edu  Wed Sep  8 15:05:58 2004
From: kumark at cshl.edu (Kiran Kumar)
Date: Wed, 8 Sep 2004 15:05:58 -0400 (EDT)
Subject: Gramene Blast Search
In-Reply-To: <718239D42CCAD611B3D700C04F070557A317D5@ICRSATY>
Message-ID: <Pine.GSO.4.05.10409081503460.11914-100000@phage.cshl.edu>

Hi Ramu,
Our blast server is of limited capacity. It cannot handle large number of
sequences at a time. Please let us know how many sequences you have to
blast and we may be able to do a batch blast for you.

regards,
Kiran

On Tue, 7 Sep 2004, Punna, Ramu (ICRISAT- IN) wrote:

>Dear Sir,
>
>Gramene blast is not working regularly.
>When we blast the sequences sometimes it is showing 'blank page' again or
>showing 'page cannot be displayed'. Everyday we are not able to blast more
>than 30-50.
>Remaining things in Gramene are working very fine.
>
>Please find if there is any problem.
>
>I look forward for your mail.
>
>With best regards,
>
>Ramu.P
>Research Scholar
>ICRISAT, Patancheru,
>India.
>



From zhz at sagc.org.cn  Mon Sep 13 09:20:48 2004
From: zhz at sagc.org.cn (zhz)
Date: Mon, 13 Sep 2004 21:20:48 +0800
Subject: about the marker position
Message-ID: <200409131311.i8DDAqY1009197@mail.sagc.org.cn>

gramene

	i am a researcher in China, last two month , i checked some markers for rice and markered them in my physical map ,but today ,i checked these markers again but to my surprise, their positions in map (Rice-Gramene TIGR Assembly 2004) are all been changed ,it must affect my research work very seriously ,so i wanna know why this happen ? thanks a lot 

????????zhz
????????zhz at sagc.org.cn
??????????2004-09-13



From dmarks at cbs.umn.edu  Fri Sep 10 14:21:12 2004
From: dmarks at cbs.umn.edu (David Marks)
Date: Fri, 10 Sep 2004 13:21:12 -0500
Subject: exactly matching sequence in rice and arabidopsis
Message-ID: <3209D12A-0356-11D9-A830-000A95BA6C6A@biosci.cbs.umn.edu>

Hi folks,

Below is pasted a large block of sequence identified by Kevin 
Silverstein here at the U of MN. This sequence is from Arabidopsis 
chromosome 5 and matches base for base a region on chromosome 10 of 
rice (Rice genome japonica TIGR).

What gives???

David Marks

50761 gtgtgttttg cgacggcaac tagaaattta gtggctgtct tgatatccaa caagaagtag
     50821 cagcatgcat gattatccaa gggaataatc aataatgtat atatagaggc 
tagactgcat
     50881 gtagtcaaat gatgactcct acttgatcat cactactgat gctatggacg 
tatttacttt
     50941 attttctttt ttttacccaa agctatagat gggatctctt tcttttatag 
gtatatgcat
     51001 gttatgccaa tcttgagcag ccattgaagg atgatgttta tagagtatgg 
actgctagtc
     51061 aaatgatgac ttctatgtta ttgtcattgc tgatgttctg gatatattta 
atattttgtt
     51121 tcctagctaa acaataagtg cagtaagaat tataggtaga gccccgcaaa 
aaaaaaaaaa
     51181 gaattatagg tagagaacag ctatagcaag gctctcctat cttatatata 
gaaagaagag
     51241 gtagcaggaa accacatccc ttcttcaacg atggaagtaa gatctttaaa 
tttgtgcttc
     51301 ctcttggttc ttgttttgct tatgagtcca gcgccaacgg caggtgtgtt 
cttactcaac
     51361 tatttttcat aacgttattg gcacacttct gcttttcgct tttcgtgcgt 
tgtcatacat




M. David Marks
Associate Professor
Department of Plant Biology
University of Minnesota
1445 Gortner Ave
St. Paul, MN 55108

(612) 625-6737
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From odla0014 at umn.edu  Wed Sep  8 13:28:38 2004
From: odla0014 at umn.edu (Wade E Odland)
Date: Wed, 08 Sep 2004 12:28:38 CDT
Subject: question on cMAP
Message-ID: <200409081728.i88HScmh002832@challenge.software.umn.edu>

Hello,

I heard from another researcher that it is possible to upload your own
mapping information into cMAP to create a graphic representitive of
homologous loci. After searching your website and can not seem to locate
this function. Is this possible? How can I access this tool?

Thanks,

Wade O


?
Wade Odland
Agronomy and Plant Genetics
411 Borlaug Hall
1991 Upper Buford Circle
St. Paul, MN 55108
ph# (612) 625-6223



From kclark at cshl.org  Tue Sep 14 11:22:14 2004
From: kclark at cshl.org (Ken Youens-Clark)
Date: Tue, 14 Sep 2004 10:22:14 -0500
Subject: question on cMAP
In-Reply-To: <200409081728.i88HScmh002832@challenge.software.umn.edu>
References: <200409081728.i88HScmh002832@challenge.software.umn.edu>
Message-ID: <DB8E75BE-0661-11D9-AA58-000393CC7E56@cshl.org>

On Sep 8, 2004, at 12:28 PM, Wade E Odland wrote:

> Hello,
>
> I heard from another researcher that it is possible to upload your own
> mapping information into cMAP to create a graphic representitive of
> homologous loci. After searching your website and can not seem to  
> locate
> this function. Is this possible? How can I access this tool?
>
> Thanks,
>
> Wade O

Wade,

It's not possible for you to upload a file to Gramene's CMap directly,  
but it is possible for you to install CMap on your own machine and then  
load whatever type of information you wish to visualize.  You can find  
out more about CMap here:

	http://www.gmod.org/cmap/

And you can download it here:

	https://sourceforge.net/project/showfiles.php? 
group_id=27707&package_id=55129

I would be happy to answer any questions you have about installing or  
using CMap.

ky



From mam94 at cornell.edu  Tue Sep 14 13:42:39 2004
From: mam94 at cornell.edu (Molly Fogleman)
Date: Tue, 14 Sep 2004 13:42:39 -0400 (EDT)
Subject: about the marker position
In-Reply-To: <200409131311.i8DDAqY1009197@mail.sagc.org.cn>
References: <200409131311.i8DDAqY1009197@mail.sagc.org.cn>
Message-ID: <1688.128.253.184.131.1095183759.squirrel@128.253.184.131>

Hello,

This has happened because Gramene updated in July 2004 to the TIGR
Assembly 2004, as you have pointed out.  The sequence alignments were
updated and therefore marker positions have changed. We hope that in the
next few years, problems such as this can be accounted for.  Let us know
if we can help with anything else and good luck with your research.



> gramene
>
> 	i am a researcher in China, last two month , i checked some markers for
> rice and markered them in my physical map ,but today ,i checked these
> markers again but to my surprise, their positions in map (Rice-Gramene
> TIGR Assembly 2004) are all been changed ,it must affect my research work
> very seriously ,so i wanna know why this happen ? thanks a lot
>
> ????????????????zhz
> ????????????????zhz at sagc.org.cn
> ????????????????????2004-09-13
>
>


Molly Fogleman
Gramene Outreach Coordinator
409 Bradfield Hall
Cornell University
Ithaca, NY 14853
(607) 255-9951



From Janet.Higgins at bbsrc.ac.uk  Thu Sep 30 07:36:34 2004
From: Janet.Higgins at bbsrc.ac.uk (Janet Higgins (JIC))
Date: Thu, 30 Sep 2004 12:36:34 +0100
Subject: Wheat markers
Message-ID: <286D8A554155B54CBFB18EF26EE2F1690157B3E7@jie2ksrv1.jic.bbsrc.ac.uk>

Please could you help me find the location of Wheat markers on the Wheat
and/or Barley genome

I have found  2 Wheat EST Markers associated with the gigantea gene
GRMG00000160561  

CD373563.1   rice location chr1  4,326,295-4,326,834 bp
BE406607.1	 rice location chr1  4,326,526-4,326,951 bp

These are shown on the Genome Browser, I have searched on Cmap but it
does not find any records on the wheat and barley maps. Is there any
mapping information on the Wheat EST markers?

Thank you for your help

Janet Higgins



From jacksond at cshl.edu  Thu Sep 30 20:58:55 2004
From: jacksond at cshl.edu (David Jackson)
Date: Thu, 30 Sep 2004 20:58:55 -0400
Subject: message for ontology curator
Message-ID: <a06020401bd825b9b7d58@[24.215.185.56]>

Dear Gramene- ontology group, I am submitting a proposal to NSF Plant 
Genome with Anne Sylvester and John Quackenbush to make GFP tagged 
lines in maize for cell biology and genomics studies.  We will be 
characterizing gene expression patterns with respect to tissue type 
and developmental stage, as well as sub-cellular localization. I was 
wondering if you have a developed ontology,especially fro 
sub-cellular localization. Is this something we could collaborate on, 
and if so could I get a letter of support for our proposal. We will 
be submitting in one week, so I can help by drafting a letter if you 
are interested,
sincerely,
Dave Jackson
-- 
Dave Jackson,
Associate Professor,
Cold Spring Harbor Laboratory,
Cold Spring Harbor,
NY 11724   USA
tel 516 367 8467
fax 516 367 8369

website http://jacksonlab.cshl.edu


