From matthews at greengenes.cit.cornell.edu  Sun Jun 15 21:10:41 2003
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Sun, 15 Jun 2003 21:10:41 -0400 (EDT)
Subject: HELP
Message-ID: <200306160110.h5G1Af0i020855@greengenes.cit.cornell.edu>

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


From rjw29 at cornell.edu  Fri Jun 13 10:16:50 2003
From: rjw29 at cornell.edu (Randall J. Wisser)
Date: Fri, 13 Jun 2003 10:16:50 -0400
Subject: Attention GRAMENE
Message-ID: <5.1.0.14.2.20030613101416.00ccbc50@postoffice2.mail.cornell.edu>

Upon searching Gramene's website an error message is returned. For example 
when one clicks on marker search the following message is returned:

Error
DBI->connect() failed: ORA-01034: ORACLE not available ORA-27101: shared 
memory realm does not exist SVR4 Error: 2: No such file or directory (DBD 
ERROR: OCISessionBegin) at /usr/local/gramene/cgi-perl/map/marker_view.cgi 
line 357




Randy
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From neeraja.vajrala at oregonstate.edu  Fri Jun 13 11:30:08 2003
From: neeraja.vajrala at oregonstate.edu (Vajrala, Neeraja)
Date: Fri, 13 Jun 2003 08:30:08 -0700
Subject: Help needed for SSRIT program!
Message-ID: <60AA1FBD310E654E9FB569BF5BFCF2216C4BB0@mtshasta.nws.oregonstate.edu>

Hi,

My name is Neeraja and I am trying to use your SSRIT program to find out
SSR's in EST's of Meadowfoam crop. I am facing problems with the
program. I am not getting consistent results for searches. Each time, I
press Find SSR's button, I am getting different result. Sometimes, when
I do not give any sequences and just press the button, then also I am
getting results. 

Can you please tell me how to rectify this problem? Or tell me how to
use the source code and run that program on my own machine?

regards
Neeraja



From shamann at grl1.grl.ars.usda.gov  Mon Jun 16 14:33:25 2003
From: shamann at grl1.grl.ars.usda.gov (Steve Hamann)
Date: Mon, 16 Jun 2003 13:33:25 -0500
Subject: SSRit working properly?
Message-ID: <000d01c33435$cc7470c0$2e963aa4@grl.ars.usda.gov>

  Genevieve DeClerck 

I have a question on the SSRit program.  This sequence below has a cgt (4) repeat.  However I cannot get the SSRit program to identify the sequence.  

I have the parameters set at (tetramer) and (5) for the number of repeats.  Shouldn't this identify this sequence?
> GCGCACTACCCGGCGCTCGCGCGGCTTTCTTTCCCAACTCCGACGAAGGCTAGCTACACC 
  ACCTGGTGCGGGCTCGTCTCCATCGCCCGCCACCCGCTCCGTCGTCGTCGTCCCCGCCGC
  GCCGATCCCGAATCGAATGGGGAGCCTGGCGTCCGAGAGGAAGGTGGTCGGGTGGGCCGC
  CAGGGACGCCACCGGACACCTCTCCCCCTACTCCTACACCCTCAGGAACACAGGCCCTGA
  AGATGTGGTGGTGAAGGTGCTCTACTGCGGGATCTGCCACACGGACATCCACCAGGCCAA
  GAACCACCTCGGGGCTTCAAAGTATCCTATGGTCCCTGGGCACGAGGTGGTCGGCGAGTG
  GTGGAGTCGGGCCCGAGTGGCCAAGTACGGCGTCGGCGACGTGGTAAGCGTCGGGGTGAT
  CGTTGGGTGCTGCCGCGAGTGThanks for any help you can provide on this.Bryan KindigerUSDA-ARSGrazinglands Research LaboratoryEl REno, OK  73036
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From rajkumar at eml.cc  Tue Jun 17 12:57:13 2003
From: rajkumar at eml.cc (Rajkumar)
Date: Tue, 17 Jun 2003 17:57:13 +0100
Subject: Help needed for SSRIT program!
In-Reply-To: <60AA1FBD310E654E9FB569BF5BFCF2216C4BB0@mtshasta.nws.oregonstate.edu>
References: <60AA1FBD310E654E9FB569BF5BFCF2216C4BB0@mtshasta.nws.oregonstate.edu>
Message-ID: <20030617165713.B6AF02EB3A@www.fastmail.fm>

Hi,

It might be some bugs in the pearl. You can find them in the source. Or
else, try this link

http://c3.biomath.mssm.edu/trf.advanced.submit.html

bye

rajkumar

----- Original message -----
From: "Vajrala, Neeraja" <neeraja.vajrala at oregonstate.edu>
To: gramene at gramene.org
Date: Fri, 13 Jun 2003 08:30:08 -0700
Subject: Help needed for SSRIT program!

Hi,

My name is Neeraja and I am trying to use your SSRIT program to find out
SSR's in EST's of Meadowfoam crop. I am facing problems with the
program. I am not getting consistent results for searches. Each time, I
press Find SSR's button, I am getting different result. Sometimes, when
I do not give any sequences and just press the button, then also I am
getting results. 

Can you please tell me how to rectify this problem? Or tell me how to
use the source code and run that program on my own machine?

regards
Neeraja



-- 
http://www.fastmail.fm - IMAP accessible web-mail


From rajkumar at eml.cc  Tue Jun 17 12:47:01 2003
From: rajkumar at eml.cc (Rajkumar)
Date: Tue, 17 Jun 2003 17:47:01 +0100
Subject: SSRit working properly?
In-Reply-To: <000d01c33435$cc7470c0$2e963aa4@grl.ars.usda.gov>
References: <000d01c33435$cc7470c0$2e963aa4@grl.ars.usda.gov>
Message-ID: <20030617164701.3AC072894F@www.fastmail.fm>

HI,

How would you expect the SSRit to pick up 4 repeats, when you set the
number of repeats as 5? Set the parameter always low (repeat>di;
number>1). Then SSRit will pick your repeat

bye

rajkumar

----- Original message -----
From: "Steve Hamann" <shamann at grl1.grl.ars.usda.gov>
To: gramene at gramene.org
Date: Mon, 16 Jun 2003 13:33:25 -0500
Subject: SSRit working properly?

  Genevieve DeClerck 

I have a question on the SSRit program.  This sequence below has a cgt
(4) repeat.  However I cannot get the SSRit program to identify the
sequence.  

I have the parameters set at (tetramer) and (5) for the number of
repeats.  Shouldn't this identify this sequence?
> GCGCACTACCCGGCGCTCGCGCGGCTTTCTTTCCCAACTCCGACGAAGGCTAGCTACACC 
  ACCTGGTGCGGGCTCGTCTCCATCGCCCGCCACCCGCTCCGTCGTCGTCGTCCCCGCCGC
  GCCGATCCCGAATCGAATGGGGAGCCTGGCGTCCGAGAGGAAGGTGGTCGGGTGGGCCGC
  CAGGGACGCCACCGGACACCTCTCCCCCTACTCCTACACCCTCAGGAACACAGGCCCTGA
  AGATGTGGTGGTGAAGGTGCTCTACTGCGGGATCTGCCACACGGACATCCACCAGGCCAA
  GAACCACCTCGGGGCTTCAAAGTATCCTATGGTCCCTGGGCACGAGGTGGTCGGCGAGTG
  GTGGAGTCGGGCCCGAGTGGCCAAGTACGGCGTCGGCGACGTGGTAAGCGTCGGGGTGAT
  CGTTGGGTGCTGCCGCGAGTGThanks for any help you can provide on this.Bryan
  KindigerUSDA-ARSGrazinglands Research LaboratoryEl REno, OK  73036

-- 
http://www.fastmail.fm - A no graphics, no pop-ups email service


From sc167 at cornell.edu  Wed Jun 18 15:17:38 2003
From: sc167 at cornell.edu (Samuel W. Cartinhour)
Date: Wed, 18 Jun 2003 15:17:38 -0400
Subject: FW: Help needed for SSRIT program!
Message-ID: <001701c335ce$47f5ebe0$8f1e5480@tc.cornell.edu>

Hi,

I confirm that the web tool at
http://www.gramene.org/gramene/searches/ssrtool sometimes produces an answer
even when no sequence is typed into the text box. I just tried it a moment
ago and produced a report concerning contig 10602-1.

Sam

-----Original Message-----
From: owner-gramene at gramene.org [mailto:owner-gramene at gramene.org] On Behalf
Of Vajrala, Neeraja
Sent: Friday, June 13, 2003 11:30 AM
To: gramene at gramene.org
Subject: Help needed for SSRIT program!

Hi,

My name is Neeraja and I am trying to use your SSRIT program to find out
SSR's in EST's of Meadowfoam crop. I am facing problems with the
program. I am not getting consistent results for searches. Each time, I
press Find SSR's button, I am getting different result. Sometimes, when
I do not give any sequences and just press the button, then also I am
getting results. 

Can you please tell me how to rectify this problem? Or tell me how to
use the source code and run that program on my own machine?

regards
Neeraja




From lstein at cshl.edu  Wed Jun 18 16:07:32 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 18 Jun 2003 16:07:32 -0400
Subject: FW: Help needed for SSRIT program!
In-Reply-To: <001701c335ce$47f5ebe0$8f1e5480@tc.cornell.edu>
References: <001701c335ce$47f5ebe0$8f1e5480@tc.cornell.edu>
Message-ID: <200306181607.32596.lstein@cshl.edu>

Hi Guys,

This is a symptom of mod_perl'ness.  There is apparently a variable that is 
not being reset between uses of the tool.  Try turning on -w and looking for 
"variable will not stay shared" warnings.

This will cause the tool to return incorrect results, so it should be a high 
priority to fix this problem.  The easiest solution is to move it to cgi-bin 
so it is out of control of mod_perl.

Lincoln

On Wednesday 18 June 2003 03:17 pm, Samuel W. Cartinhour wrote:
> Hi,
>
> I confirm that the web tool at
> http://www.gramene.org/gramene/searches/ssrtool sometimes produces an
> answer even when no sequence is typed into the text box. I just tried it a
> moment ago and produced a report concerning contig 10602-1.
>
> Sam
>
> -----Original Message-----
> From: owner-gramene at gramene.org [mailto:owner-gramene at gramene.org] On
> Behalf Of Vajrala, Neeraja
> Sent: Friday, June 13, 2003 11:30 AM
> To: gramene at gramene.org
> Subject: Help needed for SSRIT program!
>
> Hi,
>
> My name is Neeraja and I am trying to use your SSRIT program to find out
> SSR's in EST's of Meadowfoam crop. I am facing problems with the
> program. I am not getting consistent results for searches. Each time, I
> press Find SSR's button, I am getting different result. Sometimes, when
> I do not give any sequences and just press the button, then also I am
> getting results.
>
> Can you please tell me how to rectify this problem? Or tell me how to
> use the source code and run that program on my own machine?
>
> regards
> Neeraja

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From schmidt at cshl.edu  Wed Jun 18 17:32:38 2003
From: schmidt at cshl.edu (Steven Schmidt)
Date: Wed, 18 Jun 2003 17:32:38 -0400
Subject: SSRIT error
In-Reply-To: <200305121828.OAA17323@travelers.mail.cornell.edu>
References: <200305121828.OAA17323@travelers.mail.cornell.edu>
Message-ID: <200306181732.38951.schmidt@cshl.edu>

Hi Megan,

Yes, the limit is 1Mbase.

-Steve

On Monday 12 May 2003 14:28, mts28 at cornell.edu wrote:
> I am trying to run a large amount of sequence data
> through the SSRIT tool (1.2 Mbases) and I received the
> following error: "The server encountered an internal
> error or misconfiguration and was unable to complete
> your request."  I was wondering if there was a size
> limit to the length of sequence that the program can
> deal with and if so what that limit is.  Thanks for
> your help
>
> Megan Sweeney (McCouch Lab, Cornell)

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




From schmidt at cshl.edu  Wed Jun 18 18:14:40 2003
From: schmidt at cshl.edu (Steven Schmidt)
Date: Wed, 18 Jun 2003 18:14:40 -0400
Subject: ssr tool
Message-ID: <200306181814.40629.schmidt@cshl.edu>

I made some changes in the ssrtool at 
http://www.gramene.org/gramene/searches/ssrtool , so that 
"use strict;" and "use warnings;" are quiet
and so that temporary file is made in a better way.
It seems to work.
If it gives you a problem again, please send me the values
you're using.
Thanks,
Steve

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




From coee at missouri.edu  Sat Jun 21 10:54:05 2003
From: coee at missouri.edu (Ed Coe)
Date: Sat, 21 Jun 2003 09:54:05 -0500
Subject: MAIZE GENOME ASSEMBLY
Message-ID: <3EF4718D.2020605@missouri.edu>

A milestone has been reached in the Maize Mapping Project!

BAC CONTIGS AND GENETIC/PHYSICAL ANCHORING ARE NOW POSTED FOLLOWING 
COMPLETION OF PHASE I OF MANUAL EDITING!

Please help us toward refining the community resource during Phase II 
editing, by reviewing the results and status at the FPC site,
www.genome.arizona.edu/fpc/maize/
and at the iMap site,
www.maizemap.org/iMapDB/iMap.html

Your inputs, corrections, and comments are urgently sought now, and at 
any time.  Please send to me your data that have not yet been 
incorporated (e.g., probe addressing data on BACs; genetic mapping 
data), and possible corrections.

Watch for a substantially upgraded IBM2 neighbors map, and future postings.

Zealously,
Ed Coe




From liheng at itp.ac.cn  Sun Jun 22 09:02:18 2003
From: liheng at itp.ac.cn (liheng at itp.ac.cn)
Date: Sun, 22 Jun 2003 21:02:18 +0800
Subject: Where can I find the the sequences of genetic markers for Sorghum?
Message-ID: <3EF5A8DA.9040502@itp.ac.cn>

I can find markers' name but cannot find corresponding sequences. But 
where are they?



From mutengwah at yahoo.co.uk  Sun Jun 29 10:53:56 2003
From: mutengwah at yahoo.co.uk (=?iso-8859-1?q?Charles=20Mutengwa?=)
Date: Sun, 29 Jun 2003 15:53:56 +0100 (BST)
Subject: References
Message-ID: <20030629145356.90037.qmail@web13703.mail.yahoo.com>

Dear Sir/Madam

Can you kindly spell-out the full names of the
following two journals for me;

1) Mol Gen Genet

2) Kew Bull

 I would like to thank you in advance for your
assistance.

Best Regards

Charles S. Mutengwa 

________________________________________________________________________
Want to chat instantly with your online friends?  Get the FREE Yahoo!
Messenger http://uk.messenger.yahoo.com/


From pj37 at cornell.edu  Mon Jun 30 10:09:18 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 30 Jun 2003 10:09:18 -0400
Subject: References
References: <20030629145356.90037.qmail@web13703.mail.yahoo.com>
Message-ID: <3F00448E.EB7F9F51@cornell.edu>

Dear Charles,

The answer to your query is as follows.

Charles Mutengwa wrote:
> 
> Dear Sir/Madam
> 
> Can you kindly spell-out the full names of the
> following two journals for me;
> 
> 1) Mol Gen Genet

Molecular & General Genetics
The new name for this journal is  
Mol Gen Genomics (Molecular Genetics and Genomics)
http://link.springer-ny.com/link/service/journals/00438/
> 
> 2) Kew Bull
Kew Bulletin
http://www.rbgkew.org.uk/data/journals.html

Sincerely,

Pankaj
Gramene database

> 
>  I would like to thank you in advance for your
> assistance.
> 
> Best Regards
> 
> Charles S. Mutengwa
> 
> ________________________________________________________________________
> Want to chat instantly with your online friends?  Get the FREE Yahoo!
> Messenger http://uk.messenger.yahoo.com/


From downymildew at yahoo.co.in  Mon Jun  9 04:10:25 2003
From: downymildew at yahoo.co.in (=?iso-8859-1?q?Geetha=20Prashanth?=)
Date: Mon, 9 Jun 2003 09:10:25 +0100 (BST)
Subject: A request
Message-ID: <20030609081025.3435.qmail@web8205.mail.in.yahoo.com>

Dear sir/ madam,
We would like to inform you that we are working on somaclonal variation 
and their detection in pearl millet downy mildew host-pathogen 
interaction.  In this regard, we would like to discuss with the corrsponding author of this manuscrpit
"An analysis of somaclonal variation in progenies regenerated from rice calli      D. Oono1, M. Niizeki1,2, M. SENDA2, R. ISHIKAWA1, S. AKADA2  
      and T. HARADA1 
      1)Faculty of Agriculture and Life Science, Hirosaki University,  
         Hirosaki, 036-8561 Japan 
      2)Gene Research Center, Hirosaki University, Hirosaki, 036-8561 Japan"
We will be grateful if u give the e-mail ID of the corresponding author.
thanking u,
Sincerely yours,

Professor H. Shekar Shetty and Group
Downy Mildew Research Laboratory 
Dept. of Applied Botany, Seed Pathology and Biotechnology
Unversity of Mysore, Manasagangotri
Mysore-570 006, India 



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From rajkumar at eml.cc  Tue Jun 17 12:49:20 2003
From: rajkumar at eml.cc (Rajkumar)
Date: Tue, 17 Jun 2003 17:49:20 +0100
Subject: Attention GRAMENE
In-Reply-To: <5.1.0.14.2.20030613101416.00ccbc50@postoffice2.mail.cornell.edu>
References: <5.1.0.14.2.20030613101416.00ccbc50@postoffice2.mail.cornell.edu>
Message-ID: <20030617164920.560B31AFF1@www.fastmail.fm>

Hi,

Probably because, the corresponding files/folders are temporarily denied
for access. Try after sometime

bye

rajkumar

----- Original message -----
From: "Randall J. Wisser" <rjw29 at cornell.edu>
To: gramene at gramene.org
Date: Fri, 13 Jun 2003 10:16:50 -0400
Subject: Attention GRAMENE

Upon searching Gramene's website an error message is returned. For
example 
when one clicks on marker search the following message is returned:

Error
DBI->connect() failed: ORA-01034: ORACLE not available ORA-27101: shared 
memory realm does not exist SVR4 Error: 2: No such file or directory (DBD 
ERROR: OCISessionBegin) at
/usr/local/gramene/cgi-perl/map/marker_view.cgi 
line 357




Randy

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From guowenjiu at km169.net  Tue Jun 17 12:35:47 2003
From: guowenjiu at km169.net (¹ùÎÄ¾Ã)
Date: Wed, 18 Jun 2003 00:35:47 +0800 (CST)
Subject: how can I get the CDS sequence?
Message-ID: <GN969381996452.18773@email2>

Dear Sir:
   I have a set of indica genomic sequence and derived protein sequence, and I want to get the CDS of the protein. Can some one give me the idea? I'm a perl programer, I can implement the idea, if some one give me the idea.
   thank you!
   Kindly
          Wenjiu Guo(China).
 


----------------------------------------------
???????? KM169.NET ???????????? http://www.km169.net




