From gburow at lbk.ars.usda.gov  Wed Sep 17 17:24:31 2003
From: gburow at lbk.ars.usda.gov (Gloria Burow)
Date: Wed, 17 Sep 2003 16:24:31 -0500
Subject: Gramene BLAST function does not work in MAC
Message-ID: <sf688add.066@LBK.ARS.USDA.GOV>

To the Curator:
I am using  Gramene BLAST to search for sequence similarity for my work using I-Mac platform. I am having problems with the graphics for alignment.  I will obtain the results but the alignment of nucleotides between sequences are always way off.  However, I have not encounter this problem in my IBM PC.  I would like to inquire if this is really a bug in Gramene or I have to fix the setting in my I-Mac.
Thank you for your help.

Sincerely,
Dr. Gloria Burow
USDA ARS Plant Stress and Water Conservation Lab
3810 4th Street, Lubbock TX



From ware at cshl.edu  Mon Sep 22 07:10:44 2003
From: ware at cshl.edu (Ware, Doreen)
Date: Mon, 22 Sep 2003 07:10:44 -0400
Subject: Gramene BLAST function does not work in MAC
Message-ID: <39FDE54A4920D411AE0C0090274602F202D09EB1@exch01>

Dear Gloria Burow,

The individual working on the Blast Module has been away this week.  Kiran
Kumar will contact you when he has identified if there is a way to adjust
the view for the MAC platform.  Are you running OSX?

Doreen

-----Original Message-----
From: Gloria Burow [mailto:gburow at lbk.ars.usda.gov]
Sent: Wednesday, September 17, 2003 5:25 PM
To: gramene at gramene.org
Subject: Gramene BLAST function does not work in MAC


To the Curator:
I am using  Gramene BLAST to search for sequence similarity for my work
using I-Mac platform. I am having problems with the graphics for alignment.
I will obtain the results but the alignment of nucleotides between sequences
are always way off.  However, I have not encounter this problem in my IBM
PC.  I would like to inquire if this is really a bug in Gramene or I have to
fix the setting in my I-Mac.
Thank you for your help.

Sincerely,
Dr. Gloria Burow
USDA ARS Plant Stress and Water Conservation Lab
3810 4th Street, Lubbock TX


From david.horner at unimi.it  Thu Sep  4 13:02:28 2003
From: david.horner at unimi.it (David Horner)
Date: Thu, 04 Sep 2003 19:02:28 +0200
Subject: I think you have a big problem
Message-ID: <906E3800-DEF9-11D7-A5E1-000393640AEA@unimi.it>

Dear Gramene

I think you may have a big problem with the labelling (and linking) of 
your Barley TIGR GI clusters.

If you perform a blast search (with a barley est as probe) against this 
database, you recover the same hit as at the TIGR site (in terms of the 
pairwise alignment identified by the BLAST search). However, the 
contigs are labelled differently to those at TIGR. If you then follow 
the link to the construction of the contig, the sequence you recover 
bears NO RELATION AT ALL to the one that the BLAST search identified. 
In fact, these are invariably RICE sequences rather than barley 
(although NON HOMOLOGOUS to the initial probe or blast hit).

The problem may be as simple as the linking of names to sequences in 
the database, but it is a bit of a pain in the arse to find that a lot 
of work put into identifying contigs is completely invalid.

Hope this information is useful, If I am mistaken in my identification 
of a database compilation problem I apologise (and would be glad to 
understand how I have misused your site). In the meantime I will 
continue my work at TIGR.

regards

David






Dr David S. Horner

Horner's Five Thumb Postulate: Experience varies directly with 
equipment ruined.

Dipartimento di Scienze Biomolecolari e Biotecnologie
University of Milan
via Celoria, 26   -  20133 Milano, Italy
Tel. (+39) 02 50314916
Fax (+39) 02 50314912
e-mail:  david.horner at unimi.it


The   information  contained  in  this e-mail  and  any  attachments is
confidential  and  may  also  be  privileged. If you are  not the named
recipient please notify the sender  immediately and do not disclose the
contents to any other person, use it for any purpose, or store  or copy
the information in any medium.

(I've been known to send mail to the wrong person!!!!!)
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 1876 bytes
Desc: not available
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030904/3a71f1d2/attachment.bin>

From jonnyr9 at r9corporation.fsnet.co.uk  Tue Sep  9 13:33:51 2003
From: jonnyr9 at r9corporation.fsnet.co.uk (Jon Rees)
Date: Tue, 9 Sep 2003 18:33:51 +0100
Subject: Request for you to update a link on your web site.
Message-ID: <00f401c376f8$88ed35c0$b9664f51@JONS512MBP4>



Dear Sir or Madam

I am writing to you to make a request for you to update and replace an out-dated link on your page:

http://www.gramene.org/resources/    *which we think is an excellent resource!

Although "Pedro's BioMolecular Research Tools" was a great resource in its day, it has been largely superceded by
the Molecular Biology Network's site "MolBiol.Net" - which is available here: http://www.bioinformatics.vg

Here is a formatted link for you to include:
<A TITLE="Bioinformatics Tools" HREF="http://www.bioinformatics.vg">MolBiol.Net - Bioinformatics and Molecular Biology Software Portal</A>

Unlike poor old Pedro's, which has not been updated since 1996 (a long time in a fast moving discipline like bioinformatics),
MolBiol.Net is updated weekly and regularly checked for deadlinks.  It was developed partly because during my PhD I found that most of the links in Pedro's were already dead, and found this really frustrating.
Like Pedro's, however, MolBiol.Net is a free-to-use (no registration needed)and hand-curated listing of free online bioinformatics tools and other molecular biology resources.

We are a high quality site listed in Harvard's BioLinks section (http://www.mcb.harvard.edu/BioLinks/biochem.html)
as well as having been selected for inclusion in Current Web Contents by the Institute for Scientific Information,
and BIOME, the collection of high quality and evaluated resources funded by JISC (UK Joint Information Systems Committee).

If you do decide to update your link, we would appreciate an email so that we can validate it.

Kind regards,

Dr Jonathan Rees

PS. If you have any queries about this, don't hesistate to email me at pedro_update at bioinformatics.vg

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030909/bf9ecd0f/attachment.html>

From jingyu at dnalandmarks.ca  Tue Sep  9 22:32:02 2003
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Tue, 9 Sep 2003 22:32:02 -0400
Subject: TIGR Gene Index vs. GenBank UniGene?
Message-ID: <OFF3FE4C90.F7429361-ON85256D9D.000A284E@dnalandmarks.ca>

Dear Gramene,

Could you tell me the consideration that you use TIGR Gene Index but not
UniGenes from GenBank?
Thanks in advance.



From corinne.petit at biogemma.com  Tue Sep 16 07:30:31 2003
From: corinne.petit at biogemma.com (corinne.petit at biogemma.com)
Date: Tue, 16 Sep 2003 13:30:31 +0200
Subject: questions
Message-ID: <OFF99B8790.7DE6A494-ONC1256DA3.003E4640@Limagrain.com>

Hi,


I would have some data concerning the new presentation of Gramene map. I
would like to find some data concerning BAC. The last presentation allowed
us to visualize the BAC structure and position.
Now, the BAC are integrated in chromosome structure and when we examine
with a BAC nam, the window size in red  is always upper than the real size
of the BAC and it is impossible to situate exactly in the BAC as we can do
before.
Could you say me how I can proceed to do it, to find exactly the position
of the BAC on the chromosome and why not open only a map corresponding to
this BAC (as before?)
Thanks a lot for your answer (if you have understood that I want to do in
my bad english)

Best regards

Corinne Petit




From ware at cshl.edu  Thu Sep 25 09:23:02 2003
From: ware at cshl.edu (Ware, Doreen)
Date: Thu, 25 Sep 2003 09:23:02 -0400
Subject: SSRIT
Message-ID: <39FDE54A4920D411AE0C0090274602F202D09F11@exch01>

Dear Muhamet Tonguc,

Please use the following reference to site the SSRIT tool.  We will be
adding this information to the Gramene site.

Best Regards,

Doreen Ware

Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S.
Computational and experimental analysis of microsatellites in rice (Oryza
sativa L.): frequency, length variation, transposon associations, and
genetic marker potential. Genome Res. 2001 Aug;11(8):1441-52. 
PMID: 11483586 [PubMed - indexed for MEDLINE]

-----Original Message-----
From: muhammet tonguc [mailto:mt59 at cornell.edu]
Sent: Friday, August 22, 2003 2:28 PM
To: gramene at gramene.org
Subject: SSRIT



I have used SSRIT program to search for SSR motifs in DNA sequences 
in GenBank. I need to reference it for a publication and I wonder if 
you could tell me how to cite it.

Regards,
-- 
Muhammet Tonguc
Ph.D. Candidate
Cornell University-NYSAES
Horticultural Sciences
630 W. North St.
Geneva, NY 14456

Tel: 315-787-2493
Fax: 315-787-2216


From kclark at cshl.org  Thu Sep 25 10:14:54 2003
From: kclark at cshl.org (Ken Y. Clark)
Date: Thu, 25 Sep 2003 10:14:54 -0400
Subject: a question
In-Reply-To: <1461517610341971@webmail.iastate.edu>; from triffid@iastate.edu on Thu, Jul 17, 2003 at 03:06:14PM -0500
References: <1461517610341971@webmail.iastate.edu>
Message-ID: <20030925101454.A29885@cshl.org>

On Thu, Jul 17, 2003 at 03:06:14PM -0500, Carolyn Lawrence wrote:
> Hi.  I've been looking at your 'Maize - UMC 1998 - 9' map.  Why are
> some labels red and others aren't?  If there's a reason, it's not
> obvious to me (there's no key to color), but maybe I'm just not
> looking in the right places.  Could you clarify this for me?
> 
> THANKS!
> :) Carolyn

Carolyn,

I assume you're using our comparative maps (CMap)?  Can you provide a
URL for the maps you are viewing?  There is a legend at the bottom of
the image.  In the following:

http://www.gramene.org/cmap/viewer?ref_map_aid=umc-1998-9&prev_ref_map_aid=&ref_map_set_aid=umc-1998&data_source=Gramene

There are no features in red, but if I add a comparative map:

http://www.gramene.org/cmap/viewer?ref_map_start=0.00&ref_map_stop=150.40&highlight=%22txa6085%28C%29%22%2C%22txa6085%22&comparative_map_right=map_aid%3Dmiri-1&image_size=small&font_size=small&image_type=png&label_features=all&collapse_features=0&min_correspondences=&ref_map_set_aid=umc-1998&ref_map_aid=umc-1998-9&comparative_maps=&flip=&data_source=Gramene

Then some do appear in red.  In the legend at the bottom of the image
(you may have to scroll down just a bit) you will see that "features
in red have correspondences."

HTH,

ky


From pj37 at cornell.edu  Thu Sep 25 11:50:36 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 25 Sep 2003 11:50:36 -0400
Subject: Request for you to update a link on your web site.
References: <00f401c376f8$88ed35c0$b9664f51@JONS512MBP4>
Message-ID: <3F730ECB.F81EEDC0@cornell.edu>

Dear Jonathan,

Many thanks for suggestion. The resources page has been updated.
http://www.gramene.org/resources/#tools

Please confirm.

Pankaj



Jon Rees wrote:

>   Dear Sir or Madam I am writing to you to make a request for you to
> update and replace an out-dated link on your
> page: http://www.gramene.org/resources/    *which we think is an
> excellent resource! Although "Pedro's BioMolecular Research Tools" was
> a great resource in its day, it has been largely superceded by
> the Molecular Biology Network's site "MolBiol.Net" - which is
> available here: http://www.bioinformatics.vg Here is a formatted link
> for you to include:
> <A TITLE="Bioinformatics Tools"
> HREF="http://www.bioinformatics.vg">MolBiol.Net - Bioinformatics and
> Molecular Biology Software Portal</A> Unlike poor old Pedro's, which
> has not been updated since 1996 (a long time in a fast moving
> discipline like bioinformatics),
> MolBiol.Net is updated weekly and regularly checked for deadlinks.  It
> was developed partly because during my PhD I found that most of the
> links in Pedro's were already dead, and found this really frustrating.
>
> Like Pedro's, however, MolBiol.Net is a free-to-use (no registration
> needed)and hand-curated listing of free online bioinformatics tools
> and other molecular biology resources. We are a high quality site
> listed in Harvard's BioLinks section
> (http://www.mcb.harvard.edu/BioLinks/biochem.html)
> as well as having been selected for inclusion in Current Web Contents
> by the Institute for Scientific Information,
> and BIOME, the collection of high quality and evaluated resources
> funded by JISC (UK Joint Information Systems Committee). If you do
> decide to update your link, we would appreciate an email so that we
> can validate it. Kind regards, Dr Jonathan Rees PS. If you have any
> queries about this, don't hesistate to email me at
> pedro_update at bioinformatics.vg
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030925/073cfa3e/attachment.html>

From archak at cdfd.org.in  Fri Sep 26 17:07:07 2003
From: archak at cdfd.org.in (archak at cdfd.org.in)
Date: Fri, 26 Sep 2003 14:07:07 -0700 (PDT)
Subject: sequence tally?
Message-ID: <10212427.1064556460215.JavaMail.nobody@sunserver>

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  

-



From archak at cdfd.org.in  Fri Sep 26 19:14:56 2003
From: archak at cdfd.org.in (archak at cdfd.org.in)
Date: Fri, 26 Sep 2003 16:14:56 -0700 (PDT)
Subject: shaking position!!
Message-ID: <25131388.1064564127730.JavaMail.nobody@sunserver>

Hi,

this is my second mail. I tried a blast search with a test sequence and 
got the homology as "Chr 4.3 from positions 1143309 to 1143178". When I 
tried to look at the details, I was led to Chr 4.1 when I entered the above 
mentioned positions! What might be wrong? please help. 

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

-



From kumark at cshl.org  Tue Sep 30 11:56:11 2003
From: kumark at cshl.org (Kiran Kumar)
Date: Tue, 30 Sep 2003 11:56:11 -0400 (EDT)
Subject: shaking position!!
In-Reply-To: <25131388.1064564127730.JavaMail.nobody@sunserver>
Message-ID: <Pine.GSO.4.05.10309301155260.24718-100000@phage.cshl.edu>

Hi Sunil,
Could you send us the URL and we would follow up.
Kiran

On Fri, 26 Sep 2003 archak at cdfd.org.in wrote:

>Hi,
>
>this is my second mail. I tried a blast search with a test sequence and 
>got the homology as "Chr 4.3 from positions 1143309 to 1143178". When I 
>tried to look at the details, I was led to Chr 4.1 when I entered the above 
>mentioned positions! What might be wrong? please help. 
>
>Sunil Archak
>PhD Student
>Laboratory of Molecular Genetics
>CDFD
>Nacharam,
>Hyderabad-500 076, INDIA.
>Tel : +91-40-27151344  extn: 1102
>Fax : +91-40-27155610  
>
>-
>



From schmidt at cshl.edu  Tue Sep 30 12:41:11 2003
From: schmidt at cshl.edu (Steven Schmidt)
Date: Tue, 30 Sep 2003 12:41:11 -0400
Subject: sequence tally?
In-Reply-To: <10212427.1064556460215.JavaMail.nobody@sunserver>
References: <10212427.1064556460215.JavaMail.nobody@sunserver>
Message-ID: <200309301241.11857.schmidt@cshl.edu>

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




From jingyu at dnalandmarks.ca  Tue Sep 30 12:24:09 2003
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Tue, 30 Sep 2003 12:24:09 -0400
Subject: the size of gramene?
Message-ID: <OF7E12E6E2.BEC77A32-ON85256DB1.00588595@dnalandmarks.ca>

Dear Gramene curators,

Could you advise me about how much space gramene (whole) needs, if I want
to locally install it?

Thanks,

Jing



