From ana_caicedo at ncsu.edu  Wed Nov 12 13:53:52 2003
From: ana_caicedo at ncsu.edu (Ana Caicedo)
Date: Wed, 12 Nov 2003 13:53:52 -0500
Subject: chromosomal coordinates
Message-ID: <8EF8DAE8-1541-11D8-BF2A-0003939BD472@ncsu.edu>

To whom it may concern,

While locating genes in the rice genome with Gramene, I often find it 
necessary to know the coordinates of the gene with respect to the 
BAC/PAC clone on which it was sequenced. However, in the gene view page 
of Gramene I am only able to find chromosomal coordinates for the gene 
and its intron/exon structure. Since only 3 chromosomes have been 
completely assembled into contigs to date, I am worried that the 
chromosomal coordinates given for genes on other chromosomes will 
change once they are assembled into contigs. Is this true? Is there a 
way of obtaining clone coordinates for genes from Gramene.

Thank you,
Ana Caicedo


------------------------------------------------------------------------
Ana Luc?a Caicedo                               Post-Doctoral Researcher
Department of Genetics                                    (919) 515-5738
Campus Box 7614                                     ana_caicedo at ncsu.edu
North Carolina State University                   Raleigh, NC 27695-7614
------------------------------------------------------------------------




From ana_caicedo at ncsu.edu  Wed Nov 12 10:00:27 2003
From: ana_caicedo at ncsu.edu (Ana Caicedo)
Date: Wed, 12 Nov 2003 10:00:27 -0500
Subject: gene annotation
Message-ID: <F3526C73-1520-11D8-BF2A-0003939BD472@ncsu.edu>

To whom it may concern,

I have found differences in gene annotation and predicted intron/exon 
structure for rice genes found in Genbank and Gramene. I would like to 
know whichof the 2 databases is considered "safer" and more up-to-date 
on gene annotation? Are completed clone sequences being submitted 
simultaneously to both databases?

Many thanks.

Best Regards,
Ana Caicedo
------------------------------------------------------------------------
Ana Luc?a Caicedo                               Post-Doctoral Researcher
Department of Genetics                                    (919) 515-5738
Campus Box 7614                                     ana_caicedo at ncsu.edu
North Carolina State University                   Raleigh, NC 27695-7614
------------------------------------------------------------------------




From pj37 at cornell.edu  Thu Nov 13 18:09:26 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 13 Nov 2003 18:09:26 -0500
Subject: gene annotation
In-Reply-To: <F3526C73-1520-11D8-BF2A-0003939BD472@ncsu.edu>
References: <F3526C73-1520-11D8-BF2A-0003939BD472@ncsu.edu>
Message-ID: <3FB40F26.1020703@cornell.edu>

Dear Ana,

The problem you are citing is an obvious one. In Gramene the data is update 
every three months. There is a possibility that with in this 3 month period, the 
BAC clones submitted to the GenBank by sequencing centers may under go 
revision/updates with a new or a modified gene model for a given gene. As of 
this time, when the rice genome is being assembled, this situation is going to 
remain fluid for a while and we do not foresee any quick resolutions. Gramene 
provides its own annotation of gene models based on predictions by the Fgenesh 
program and alignments to the ESTs and unigene sets/clusters. Additionally we 
carry all the annotation provided by the sequencing centers.

We hope this will address your question.

Sincerely
Pankaj
gramene at gramene.org


Ana Caicedo wrote:

> To whom it may concern,
> 
> I have found differences in gene annotation and predicted intron/exon 
> structure for rice genes found in Genbank and Gramene. I would like to 
> know whichof the 2 databases is considered "safer" and more up-to-date 
> on gene annotation? Are completed clone sequences being submitted 
> simultaneously to both databases?
> 
> Many thanks.
> 
> Best Regards,
> Ana Caicedo
> ------------------------------------------------------------------------
> Ana Luc?a Caicedo                               Post-Doctoral Researcher
> Department of Genetics                                    (919) 515-5738
> Campus Box 7614                                     ana_caicedo at ncsu.edu
> North Carolina State University                   Raleigh, NC 27695-7614
> ------------------------------------------------------------------------
> 




From mizuno14 at totoville.net  Fri Nov 14 15:10:20 2003
From: mizuno14 at totoville.net (Mary Osenga)
Date: Fri, 14 Nov 2003 14:10:20 -0600
Subject: citation
Message-ID: <007301c3aaeb$54ffe9c0$b2758186@ndsu.nodak.edu>

How does one cite the use of the Gramene datebase in a publication?

Thanks,

Mary Osenga







-- - -- - -- - -- - -- - -- - -- - -- - -- - -- - -- - -- 
Mary Osenga
zenga2 at alum.ndsu.nodak.edu
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From pj37 at cornell.edu  Thu Nov 20 14:57:36 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 20 Nov 2003 14:57:36 -0500
Subject: citation
In-Reply-To: <007301c3aaeb$54ffe9c0$b2758186@ndsu.nodak.edu>
References: <007301c3aaeb$54ffe9c0$b2758186@ndsu.nodak.edu>
Message-ID: <3FBD1CB0.2030705@cornell.edu>

Gramene: a resource for comparative grass genomics.
Nucleic Acids Research, 2002, Vol. 30, No. 1, 103-105
http://brie2.cshl.org:8082/about/index.html#publications


Thanks for using Gramene.

Pankaj


Mary Osenga wrote:

> How does one cite the use of the Gramene datebase in a publication?
>  
> Thanks,
>  
> Mary Osenga
>  
>  
>  
>  
>  
>  
> 
> -- - -- - -- - -- - -- - -- - -- - -- - -- - -- - -- - --
> Mary Osenga
> zenga2 at alum.ndsu.nodak.edu <mailto:zenga2 at alum.ndsu.nodak.edu>

-- 




From ware at cshl.edu  Fri Nov 21 09:05:47 2003
From: ware at cshl.edu (Ware, Doreen)
Date: Fri, 21 Nov 2003 09:05:47 -0500
Subject: citation
Message-ID: <39FDE54A4920D411AE0C0090274602F202D0A258@exch01>

Dear Mary,
 
To cite  the database please use the  reference below. If you have any other
questions about the database or constructive feedback please contact us.
Thank you for using Gramene. 
 
Doreen 
 
Ware, D., P. Jaiswal, et al. (2002). "Gramene: a resource for comparative
grass genomics." Nucleic Acids Res 30(1): 103-5.

-----Original Message-----
From: Mary Osenga [mailto:mizuno14 at totoville.net]
Sent: Friday, November 14, 2003 3:10 PM
To: gramene at gramene.org
Subject: citation


How does one cite the use of the Gramene datebase in a publication?
 
Thanks,
 
Mary Osenga
 
 
 
 
 
 

-- - -- - -- - -- - -- - -- - -- - -- - -- - -- - -- - -- 
Mary Osenga
zenga2 at alum.ndsu.nodak.edu <mailto:zenga2 at alum.ndsu.nodak.edu> 

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From yann-francois.bizouerne at bayercropscience.com  Mon Nov 24 04:25:25 2003
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Mon, 24 Nov 2003 10:25:25 +0100
Subject: Problem with the gramene ftp
Message-ID: <OF7A7A3CC8.7FA3211B-ONC1256DE8.00333BD2-C1256DE8.0033C3FE@bayer.de>





Hello,

our team wants to install Gramene locally. So after reading the documentation
find on your website, I try to donwoad the different packages.
All works well except for this one :
ftp://ftp.gramene.org/pub/gramene/software/website/gramene-rel-X-Y.tgz
I could go to the directory ftp://ftp.gramene.org/pub/gramene/software, but when
I want to access the website/ directory it doesn't works.
Do I need a password for this directory ? Or could I find the package
(gramene-rel-X-Y.tgz) in an other location ?

Thanks in advance for your answer.


Yann-Fran?ois BIZOUERNE
BioInformatic Team
BAYER CropScience
1, rue Pierre Fontaine
91058 Evry Cedex
FRANCE
Phone:      33-(0) 1-69-47-61-56
FAX:        33-(0) 1-69-47-61-42
E-mail:     yann-francois.bizouerne at bayercropscience.com
Intranet: http://bioinfo.evry.fr.bayercropscience/




From lsmith at biomail.ucsd.edu  Fri Nov 21 22:07:34 2003
From: lsmith at biomail.ucsd.edu (Laurie G. Smith)
Date: Fri, 21 Nov 2003 19:07:34 -0800
Subject: question
Message-ID: <f05200f37bbe47e41c16e@[132.239.144.75]>

Dear Gramene,

Your site is awesome!

However I've been struggling for the last two hours to figure out how 
to do something that seems like it should be very simple. Basically 
what I'm trying to do is to determine map locations of maize genes 
for which I know the location of the rice homolog.

Here is the basic flow of what I'm trying to do:

locate rice gene of interest based on homology to a maize gene --->
look for markers in the immediate vicinity of the rice gene that are 
also on some sort of maize map (some are on the maize IBM 2003 
neighbors map, but the most plentiful and useful are those mapped 
onto maize FPC 2003 physical maps) -->
find out where the maize FPC map is on the maize IBM 2003 neighbors map

I can see there are many correspondences between the maize IBM 
Neighbors 2003 map and the AGI FPC 2003 physical maps - using the 
Matrix, I can view them chromosome by chromosome, but there are 
hundreds per chromosome, so scanning these diagrams is a totally 
inefficient way to find a specific FPC and see where it is on the IBM 
Neighbors map. I figured out how to use map viewer to choose a small 
region of a maize chromosome I designate and find the FPC maps with 
correspondences in that region. But I want to search the other way 
around - to designate a specific AGI FPC 2003 map (using their names, 
like ctg514.0 or ctg1063.0) and find out whether there are any 
markers on it that are also on the maize IBM Neighbors map.  In other 
words, for any given FPC map I'm interested in, how can I figure out 
whether and where it maps onto the maize IBM Neighbors 2003 map?

Thanks for any help you can give me,

Laurie Smith
-- 
Laurie G. Smith
Associate Professor
Division of Biological Sciences 0116
U.C. San Diego
9500 Gilman Drive
Rm. 5135 Muir Biology
La Jolla, CA  92093-0116
tel: (858)-822-2531
fax: (858)-534-7108
email: lsmith at biomail.ucsd.edu



From kclark at cshl.org  Mon Nov 24 15:43:39 2003
From: kclark at cshl.org (Ken Y. Clark)
Date: Mon, 24 Nov 2003 15:43:39 -0500
Subject: question
In-Reply-To: <f05200f37bbe47e41c16e@[132.239.144.75]>; from lsmith@biomail.ucsd.edu on Fri, Nov 21, 2003 at 07:07:34PM -0800
References: <f05200f37bbe47e41c16e@[132.239.144.75]>
Message-ID: <20031124154339.A28674@cshl.org>

On Fri, Nov 21, 2003 at 07:07:34PM -0800, Laurie G. Smith wrote:
[...]
> markers on it that are also on the maize IBM Neighbors map.  In other 
> words, for any given FPC map I'm interested in, how can I figure out 
> whether and where it maps onto the maize IBM Neighbors 2003 map?

Laurie,

I'm sorry this is proving difficult for you.  I will take a stab at
answering your question since I wrote the comparative map software;
however, I'm not a biologist, so my answer may be incomplete.  That
said, I wonder if you shouldn't start off restricting the matrix view
to the "Maize-IBM Neighbors 2003" map set like so:

    http://www.gramene.org/cmap/matrix?species_aid=;map_set_aid=ibm2n

>From there you can see that the number of correspondences from any of
the physical map sets to each of the chromosomes of maize.  Clicking
on the numbers in the matrix will take you to a view where a maize map
is the "reference" map and the FPC contigs line up where the
correspondences exists, like so:

    http://www.gramene.org/cmap/viewer?ref_map_set_aid=ibm2n;ref_map_aid=ibm2n1;comparative_maps=1%3dmap_set_aid%3dcf03

That can be confusing to look at, so perhaps you'd like to drop off
the contigs with only 1 correspondence to the reference map.  Just
indicate this as the "Min. No. Correspondences" argument, like this:

    http://www.gramene.org/cmap/viewer?ref_map_start=-55.80&ref_map_stop=1272.50&highlight=%22txa6085%28C%29%22%2C%22txa6085%22&image_size=small&font_size=small&image_type=png&label_features=all&collapse_features=0&min_correspondences=2&ref_map_set_aid=ibm2n&ref_map_aid=ibm2n1&comparative_maps=1%3Dmap_set_aid%3Dcf03&flip=&data_source=Gramene

Does that make it easier to find what you're interested in?

ky


From schmidt at cshl.edu  Tue Nov 25 11:45:26 2003
From: schmidt at cshl.edu (Steven Schmidt)
Date: Tue, 25 Nov 2003 11:45:26 -0500
Subject: Problem with the gramene ftp
In-Reply-To:  <OF7A7A3CC8.7FA3211B-ONC1256DE8.00333BD2-C1256DE8.0033C3FE@bayer.de>
References: <OF7A7A3CC8.7FA3211B-ONC1256DE8.00333BD2-C1256DE8.0033C3FE@bayer.de>
Message-ID: <200311251145.26339.schmidt@cshl.edu>

Hello,

The directory permissions look ok to me, but the package needs to be updated.
I will fix it up by Monday, and make sure it can be downloaded from outside 
the lab.

-Steve

On Monday 24 November 2003 04:25 am, 
yann-francois.bizouerne at bayercropscience.com wrote:
> Hello,
>
> our team wants to install Gramene locally. So after reading the
> documentation find on your website, I try to donwoad the different
> packages.
> All works well except for this one :
> ftp://ftp.gramene.org/pub/gramene/software/website/gramene-rel-X-Y.tgz
> I could go to the directory ftp://ftp.gramene.org/pub/gramene/software, but
> when I want to access the website/ directory it doesn't works.
> Do I need a password for this directory ? Or could I find the package
> (gramene-rel-X-Y.tgz) in an other location ?
>
> Thanks in advance for your answer.
>
>
> Yann-Fran?ois BIZOUERNE
> BioInformatic Team
> BAYER CropScience
> 1, rue Pierre Fontaine
> 91058 Evry Cedex
> FRANCE
> Phone:      33-(0) 1-69-47-61-56
> FAX:        33-(0) 1-69-47-61-42
> E-mail:     yann-francois.bizouerne at bayercropscience.com
> Intranet: http://bioinfo.evry.fr.bayercropscience/

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977




From PolaccoM at missouri.edu  Mon Nov 24 17:49:34 2003
From: PolaccoM at missouri.edu (Mary Polacco)
Date: Mon, 24 Nov 2003 16:49:34 -0600
Subject: question
In-Reply-To: <f05200f37bbe47e41c16e@[132.239.144.75]>
Message-ID: <BBE7E71E.9FF6%PolaccoM@missouri.edu>

Hi Laurie,
We are in the final throes of building a process to place maize physical FPC
map markers onto IBM neighbors. This is in addition to refining the
genetically mapped markers on IBM neighbors where the physical map provides
a more precise ordering.

Another add to Neighbors will be the inclusion  of the Genetic map mutants,
a lower resolution map set, and with few correspondences with the higher
resolution maps, so it is really 'beware city' for those guys.

The  new neighbors should go on-line soon, and I will let you know when we
it appears at MaizeGDB. It should provide the sort of correspondances you
want to see when it gets ported into Gramene.

-mary


-- 
Mary Polacco, PhD
Research Geneticist/Curator MaizeGDB
USDA/ARS Plant Genetics Research Unit
203 Curtis Hall
Adjunct Associate Professor
Dept. of Agronomy, Plant Sciences Unit
University of Missouri
Columbia, MO 65211
Phone: 573 884 7873
FAX: 573 884 7850



On 11/21/03 9:07 PM, "Laurie G. Smith" <lsmith at biomail.ucsd.edu> wrote:

> Dear Gramene,
> 
> Your site is awesome!
> 
> However I've been struggling for the last two hours to figure out how
> to do something that seems like it should be very simple. Basically
> what I'm trying to do is to determine map locations of maize genes
> for which I know the location of the rice homolog.
> 
> Here is the basic flow of what I'm trying to do:
> 
> locate rice gene of interest based on homology to a maize gene --->
> look for markers in the immediate vicinity of the rice gene that are
> also on some sort of maize map (some are on the maize IBM 2003
> neighbors map, but the most plentiful and useful are those mapped
> onto maize FPC 2003 physical maps) -->
> find out where the maize FPC map is on the maize IBM 2003 neighbors map
> 
> I can see there are many correspondences between the maize IBM
> Neighbors 2003 map and the AGI FPC 2003 physical maps - using the
> Matrix, I can view them chromosome by chromosome, but there are
> hundreds per chromosome, so scanning these diagrams is a totally
> inefficient way to find a specific FPC and see where it is on the IBM
> Neighbors map. I figured out how to use map viewer to choose a small
> region of a maize chromosome I designate and find the FPC maps with
> correspondences in that region. But I want to search the other way
> around - to designate a specific AGI FPC 2003 map (using their names,
> like ctg514.0 or ctg1063.0) and find out whether there are any
> markers on it that are also on the maize IBM Neighbors map.  In other
> words, for any given FPC map I'm interested in, how can I figure out
> whether and where it maps onto the maize IBM Neighbors 2003 map?
> 
> Thanks for any help you can give me,
> 
> Laurie Smith



