From C.VIJAYAKUMAR at CGIAR.ORG  Mon Jun  3 09:36:57 2002
From: C.VIJAYAKUMAR at CGIAR.ORG (Vijayakumar, C.H.M.)
Date: Mon, 03 Jun 2002 06:36:57 -0700
Subject: Rice Bibliography
Message-ID: <3EA5C75212CDD511B74100508BE095769FBF73@mail.irri.cgiar.org>

 <<Rice Bibliography.htm>>  
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From ware at cshl.edu  Tue Jun  4 09:21:22 2002
From: ware at cshl.edu (Ware, Doreen)
Date: Tue, 4 Jun 2002 09:21:22 -0400 
Subject: Rice Bibliography
Message-ID: <39FDE54A4920D411AE0C0090274602F2012D2949@exch01.cshl.org>

Dear Vijayakumar,

Can you please tell me the reference of the email you have sent.

Sincerely,


Doreen Ware
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724
Phone: (516) 367-6979
Fax:  (516) 367-8389
E-mail: ware at cshl.org

-----Original Message-----
From: Vijayakumar, C.H.M. [mailto:C.VIJAYAKUMAR at CGIAR.ORG]
Sent: Monday, June 03, 2002 9:37 AM
To: 'gramene at gramene.org'
Subject: Rice Bibliography

 <<Rice Bibliography.htm>> 


From changku at stein.cshl.org  Mon Jun  3 17:51:42 2002
From: changku at stein.cshl.org (Kuan Y. Chang)
Date: Mon, 3 Jun 2002 17:51:42 -0400 (EDT)
Subject: question about sequence table
Message-ID: <Pine.GSO.4.05.10206031725030.11571-100000@phage.cshl.org>

Hi all,

I have a question about your sequence table.  I understand the need to
have sequence ontology, but I don't understand why GO decides to keep the
real sequences in the database.  In the May 2002 GO release, the sequence
data file is about 24 MB.  However, it seems that all of the 24 MB data
can be found thru their Swiss-Prot accession numbers.  Could someone
please explain why you keep the sequence data?  Thank you very much!

Kuan



From C.VIJAYAKUMAR at CGIAR.ORG  Mon Jun  3 09:35:13 2002
From: C.VIJAYAKUMAR at CGIAR.ORG (Vijayakumar, C.H.M.)
Date: Mon, 03 Jun 2002 06:35:13 -0700
Subject: regarding RG64 PCR marker inforamtion
Message-ID: <3EA5C75212CDD511B74100508BE095769FBF72@mail.irri.cgiar.org>

RG64 STS in rice or SAP or STS was first published in TAG by Hittalmani et
al, 1995 in TAG 91(1)9-14pp. issue. This was the first time that RG 64clone
from Cornell University  was entirely sequenced and published and primer
sequece published. It was also the first time that it was used as PCR primer
to detect blast resistance gene Pi-2. I would appreciate if this information
goes in the data base. It is written that forward and reverse primers re
unknown unknown. The above paper describes all the inforamtion that was
publsihed in as popular journal as TAG.


From noelyap at ascus.plbr.cornell.edu  Tue Jun  4 12:58:08 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Tue, 4 Jun 2002 12:58:08 -0400
Subject: regarding RG64 PCR marker inforamtion
In-Reply-To: <3EA5C75212CDD511B74100508BE095769FBF72@mail.irri.cgiar.org>
References: <3EA5C75212CDD511B74100508BE095769FBF72@mail.irri.cgiar.org>
Message-ID: <15612.61856.328633.343206@ascus.plbr.cornell.edu>

Dear Dr Vijayakumar,

Thank you for bringing this to our attention.  We are in the process
of updating our marker data and this information will be included in a
future release.

Sincerely,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From Leszek at missouri.edu  Wed Jun  5 18:48:25 2002
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Wed, 5 Jun 2002 17:48:25 -0500
Subject: Conference Call - Update
Message-ID: <E8C167D6966BBC44903B6B2C3BDE57C171CB60@col-mailnode04.col.missouri.edu>

Hi again colleagues

Regarding the phone conference considered for next week - thanks for your responses. 

One change: I'd like to move it forward by 1 hour - to 3 p.m. (CST). Can  the rest of you accommodate this?? I'll email you the connection details later in the week (as before).

As mentioned in the email yesterday, I'd like the focus of this conference call to be on the proposal I'm drafting, for funding for the Plant Ontology Consortium, to be submitted to the NSF (by June 28). 

I've provided some 'Guiding Questions' below to facilitate the development of your contributions to the conference call. Besides being able to air your thoughts on these questions, the conf. call will probably stimulate other thoughts - you're encouraged to share these with me either after the call (email) or even before if that suits you better (email) of if you won't be able to participate in the conf. call (e.g. IRRI folk) - (email).

TAIR folk - I know that you aren't able to be collaborators of the POC at this time (although very much associated with the work of the POC). But I do want to keep you 'in the loop' of our ongoing dialogue. So feel free to 'listen in'. And do feel free to respond to any of the 'guiding questions' - your ongoing input is highly valued & much appreciated.

Attached to this note is a copy of the previous proposal to the NSF (sorry about the size!). The resubmission is likely to be significantly different although built, in part, on the previous (attached) proposal. Most of the pages probably don't need to be perused (sighs of relief...). Probably pages 1-8 (Project Description) & some of the Budget summary pages would be most appropriate for reading.

Guiding questions:

1. What evidence would you like to see included in the proposal (or linked to?) to demonstrate that we can go beyond a controlled vocabulary to a full ontology?

2. The previous submission was criticized for not including more of the GO philosophy in the proposal. What else of the GO philosophy do you think should be included to cancel this perception?

3. To quote from the Panel Summary of the previous submission: "There is a need to identify the major systems descriptions that will be revised or created de novo to cause a plant ontology to form." What's your response to this perceived "need"?

4. Please comment on what plans you would like to see in place to make the 'consortium' real.

5. I'll be structuring the budget so that it fits within (or close to within) the $500,000 figure. What components of the previous budget do you consider essential/should be kept? What new component(s) would you like to see included?

Thanks for your ongoing participation in the POC - pushing back the frontiers towards interoperability.

Sincerely,
- Leszek Vincent
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
Ph/Fax (Home): (573) 441-1228; 
Email: Leszek at missouri.edu
Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
(http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
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From Leszek at missouri.edu  Thu Jun  6 14:27:26 2002
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Thu, 6 Jun 2002 13:27:26 -0500
Subject: Copy of NSF reviewers' comments
Message-ID: <E8C167D6966BBC44903B6B2C3BDE57C171CB63@col-mailnode04.col.missouri.edu>


Hi Colleagues

Pankaj asked if I would consider providing all of you with a copy of the reviewers' comments on the previous submission to the NSF - the idea being that this info. might assist you in providing feedback during the conference call or via email. I'm sure the snippets I shared during the PAMG meeting & email are an unsatisfactory representation. So, I've done the OCR scanning & removed all my many pencilled annotations. So the attached copy contains all the original text. I've cleaned my email-box in anticipation of your feedback/suggestions ;-)

TAIR folk - you're most welcome to put this info. in your 'melting pot' of any email feedback you'd like to provide me (assuming you won't be participating in the conf. call ?).

- Leszek
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
Ph/Fax (Home): (573) 441-1228; 
Email: Leszek at missouri.edu
Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
(http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
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From rhee at acoma.Stanford.EDU  Mon Jun 10 18:22:44 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Mon, 10 Jun 2002 15:22:44 -0700 (PDT)
Subject: Conference Call No. & Agenda
In-Reply-To: <E8C167D6966BBC44903B6B2C3BDE57C1758729@col-mailnode04.col.missouri.edu>
Message-ID: <Pine.GSO.4.44.0206101516000.3576-100000@acoma.Stanford.EDU>

Hi, Vincent,

TAIR would be happy to participate as collaborators of POC on your
proposal if the following issues are addressed and agreed upon:

1. What is the scientific goal of POC?

2. Which groups are members of POC and what is each member committed to
do for POC?

Cheers,
Sue

On Mon, 10 Jun 2002, Vincent, Leszek wrote:

> Dear Colleagues,
>
> The number for you to use to participate in the conference call tomorrow (Tuesday, 11 June) at 3:00 p.m. (CST; 15:00 CST) is: (573) 884-7102. [I've booked 1.5 hrs but hope we'll be done in less time]
>
> Provisional Agenda:
>
> 1. Welcome
>
> 2. Comments on theme: "Enhancement of communications, collaborations and the development of plant-based ontologies and controlled vocabularies."
> [Background: Title of proposed project is 'Plant Ontology Consortium'; to be submitted to the Research Coordination Networks Program of the NSF (NSF 00-56)]
>
> 3. Your responses to the following guiding questions:
>
> 	3.1. What evidence would you like to see included in the proposal (or linked to?) to demonstrate that we can go beyond a controlled vocabulary to a full ontology?
>
> 	3.2. The previous submission was criticized for not including more of the GO philosophy in the proposal. What else of the GO philosophy do you think should be included to cancel this perception?
>
> 	3.3. To quote from the Panel Summary of the previous submission: "There is a need to identify the major systems descriptions that will be revised or created de novo to cause a plant ontology to form." What's your response to this perceived "need"?
>
> 	3.4. Please comment on what plans you would like to see in place to make the 'consortium' real.
>
> 	3.5. I'll be structuring the budget so that it fits within (or close to within) the $500,000 figure (over 5yrs); estimate $50K-$60K available for each of 5 yrs. What components of the previous budget do you consider essential/should be kept? What new component(s) would you like to see included?
>
> 4. Co-PI(s) on grant - for discussion.
>
> 5. Suggestions on authors of 'Letters of Support'.
>
> 6. Tentative time-table:
>
> 	06/11-17/'02 - submission of other responses to Guiding Questions & other inputs (ALL)
>
> 	06/18/'02 - completion of draft of 'Project Description' & outline of budget (PLDV) - to be emailed to all on list - for feedback
>
> 	06/21/'02 - receipt of feedback to drafts (ALL to PLDV)
>
> 	06/21/'02 - receipt of Letters of Support & docs from Co-PI('s) (to PLDV)
>
> 	06/24-27/'02 - any necessary reworking of docs (PLDV) & uploading of components via FastLane (NSF)
>
> 	06/28/'02 - electronic submission to NSF via FastLane
>
> 7. Any other matters that you would like to discuss...
>
>
>
>
> I look forward to 'meeting' with you tomorrow.
>
> Sincerely,
> - Leszek
>
> xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> P. Leszek D. Vincent Ph.D., FLS
> Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
> Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
> Ph/Fax (Home): (573) 441-1228;
> Email: Leszek at missouri.edu
> Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> (http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
> xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
>

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------



From Leszek at missouri.edu  Mon Jun 10 18:10:34 2002
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Mon, 10 Jun 2002 17:10:34 -0500
Subject: Conference Call No. & Agenda
Message-ID: <E8C167D6966BBC44903B6B2C3BDE57C1758729@col-mailnode04.col.missouri.edu>

Dear Colleagues,

The number for you to use to participate in the conference call tomorrow (Tuesday, 11 June) at 3:00 p.m. (CST; 15:00 CST) is: (573) 884-7102. [I've booked 1.5 hrs but hope we'll be done in less time]

Provisional Agenda:

1. Welcome

2. Comments on theme: "Enhancement of communications, collaborations and the development of plant-based ontologies and controlled vocabularies." 
[Background: Title of proposed project is 'Plant Ontology Consortium'; to be submitted to the Research Coordination Networks Program of the NSF (NSF 00-56)]

3. Your responses to the following guiding questions:

	3.1. What evidence would you like to see included in the proposal (or linked to?) to demonstrate that we can go beyond a controlled vocabulary to a full ontology?

	3.2. The previous submission was criticized for not including more of the GO philosophy in the proposal. What else of the GO philosophy do you think should be included to cancel this perception?

	3.3. To quote from the Panel Summary of the previous submission: "There is a need to identify the major systems descriptions that will be revised or created de novo to cause a plant ontology to form." What's your response to this perceived "need"?

	3.4. Please comment on what plans you would like to see in place to make the 'consortium' real.

	3.5. I'll be structuring the budget so that it fits within (or close to within) the $500,000 figure (over 5yrs); estimate $50K-$60K available for each of 5 yrs. What components of the previous budget do you consider essential/should be kept? What new component(s) would you like to see included?

4. Co-PI(s) on grant - for discussion.

5. Suggestions on authors of 'Letters of Support'.

6. Tentative time-table:

	06/11-17/'02 - submission of other responses to Guiding Questions & other inputs (ALL)

	06/18/'02 - completion of draft of 'Project Description' & outline of budget (PLDV) - to be emailed to all on list - for feedback

	06/21/'02 - receipt of feedback to drafts (ALL to PLDV)

	06/21/'02 - receipt of Letters of Support & docs from Co-PI('s) (to PLDV)

	06/24-27/'02 - any necessary reworking of docs (PLDV) & uploading of components via FastLane (NSF)

	06/28/'02 - electronic submission to NSF via FastLane

7. Any other matters that you would like to discuss...




I look forward to 'meeting' with you tomorrow.

Sincerely,
- Leszek

xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
Ph/Fax (Home): (573) 441-1228; 
Email: Leszek at missouri.edu
Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
(http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox


From jeffery.shen at ccmail.nevada.edu  Wed Jun 12 20:58:44 2002
From: jeffery.shen at ccmail.nevada.edu (jeffery.shen at ccmail.nevada.edu)
Date: Wed, 12 Jun 2002 17:58:44 -0700
Subject: question about rice books
Message-ID: <OF4B340223.9250D2FD-ON88256BD7.0004D4DF@nevada.edu>


Dear Grameners,

I am new faculty member at University of Nevada at Las Vegas.  While I was
a student at Washington University in St. Louis and a Senior Scientist in
Monsanto, I worked on the molecular mechanism of ABA response, mainly in
barley and soybean.  Recently, I am very much interested in rice because of
the availability of its genome sequences. I like to buy a few good books on
rice biology -- anatomy, development, genetics etc.  Someone recommended
the following book to me.

"Science of the rice plant", edited by Takane Matsuo, Yuzo Futsuhara, Fumio
Kikuchi, and Hikoyuki
Yamaguchi. Published in 1997, ISBN4-540-96010-5

However, I couldn't find where in the United States I can purchase this
book.  Please let me know if you know where I can buy this book or you have
other good rice book information.

Thank you very much for your help in advance.

Best regards,




Jeff  Qingxi Shen
Assistant Professor
Department of Biological Sciences
Mailstop 4004
University of Nevada
4505 Maryland Pkwy
Las Vegas, NV89154
Tel: (702) 895-4704
Fax: (702) 895-3956
jeffery_shen at ccmail.nevada.edu
www.unlv.edu/faculty/jeffshen





From pj37 at cornell.edu  Thu Jun 13 13:30:15 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 13 Jun 2002 13:30:15 -0400
Subject: question about rice books
References: <OF4B340223.9250D2FD-ON88256BD7.0004D4DF@nevada.edu>
Message-ID: <3D08D6A7.28B28AE4@cornell.edu>

Dear Jeffery,

You can buy the book "Science of the rice plant", from
http://www.ruralnet.or.jp/E/srp/

or or else you can ask for an interlibrary loan for this book from Cornell
University.

There are many more  good books covering the topics you mentioned on rice are
available from 
Barnes & Noble (www.books.com) 
Amazon.com
IRRI at http://www.irri.org/pubcat2000/pubcontents.htm

Sincerely

Pankaj

jeffery.shen at ccmail.nevada.edu wrote:
> 
> Dear Grameners,
> 
> I am new faculty member at University of Nevada at Las Vegas.  While I was
> a student at Washington University in St. Louis and a Senior Scientist in
> Monsanto, I worked on the molecular mechanism of ABA response, mainly in
> barley and soybean.  Recently, I am very much interested in rice because of
> the availability of its genome sequences. I like to buy a few good books on
> rice biology -- anatomy, development, genetics etc.  Someone recommended
> the following book to me.
> 
> "Science of the rice plant", edited by Takane Matsuo, Yuzo Futsuhara, Fumio
> Kikuchi, and Hikoyuki
> Yamaguchi. Published in 1997, ISBN4-540-96010-5
> 
> However, I couldn't find where in the United States I can purchase this
> book.  Please let me know if you know where I can buy this book or you have
> other good rice book information.
> 
> Thank you very much for your help in advance.
> 
> Best regards,
> 
> Jeff  Qingxi Shen
> Assistant Professor
> Department of Biological Sciences
> Mailstop 4004
> University of Nevada
> 4505 Maryland Pkwy
> Las Vegas, NV89154
> Tel: (702) 895-4704
> Fax: (702) 895-3956
> jeffery_shen at ccmail.nevada.edu
> www.unlv.edu/faculty/jeffshen


From pj37 at cornell.edu  Fri Jun 14 11:33:55 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 14 Jun 2002 11:33:55 -0400
Subject: Help on curation of STAD_ORYSA
Message-ID: <3D0A0CE3.60C18D8F@cornell.edu>

Hi Tanya,
Sender: owner-gramene at stein.cshl.org
Precedence: bulk
Reply-To: gramene at gramene.org, Pankaj Jaiswal <pj37 at cornell.edu>

I am confused on how to curate a rice entry which has a similarity to
Arabidopsis protein
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=genbank&term=%22AF395441%22

Which biological process should I include for 
activator signal for Jasmonic acid dependent defence response

In Arabidopsis, the enzyme catalyzes a desaturation step that is required for
Jasmonic acid biosynthesis. Also acts as an activator signal for Jasmonic acid
dependent defence response at the time of pathogen interaction


Annotation for rice entry 
http://www.gramene.org/perl/protein_search?protein_id=78051

I have discarded the electronic annotation from Interpro matches.

Molecular Function|acyl-[acyl-carrier-protein]
desaturase|GO:0045300|GR_REF:62|ISS
Biological Process|fatty acid elongation, unsaturated fatty
acid|GO:0019368|GR_REF:62|ISS
Cellular Component|plastid stroma|GO:0009532|GR_REF:62|ISS
Cellular Component|chloroplast stroma|GO:0009570|GR_REF:62|ISS

Also we need to add GO terms 
Fatty acid desaturase 
and 
add "stearoyl ACP desaturase" as synonym for acyl-[acyl-carrier-protein]
desaturase; GO:0045300

Thanks
Pankaj

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From pj37 at cornell.edu  Fri Jun 14 11:33:55 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 14 Jun 2002 11:33:55 -0400
Subject: Help on curation of STAD_ORYSA
Message-ID: <3D0A0CE3.60C18D8F@cornell.edu>


Hi Tanya,

I am confused on how to curate a rice entry which has a similarity to
Arabidopsis protein
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=genbank&term=%22AF395441%22

Which biological process should I include for 
activator signal for Jasmonic acid dependent defence response

In Arabidopsis, the enzyme catalyzes a desaturation step that is required for
Jasmonic acid biosynthesis. Also acts as an activator signal for Jasmonic acid
dependent defence response at the time of pathogen interaction


Annotation for rice entry 
http://www.gramene.org/perl/protein_search?protein_id=78051

I have discarded the electronic annotation from Interpro matches.

Molecular Function|acyl-[acyl-carrier-protein]
desaturase|GO:0045300|GR_REF:62|ISS
Biological Process|fatty acid elongation, unsaturated fatty
acid|GO:0019368|GR_REF:62|ISS
Cellular Component|plastid stroma|GO:0009532|GR_REF:62|ISS
Cellular Component|chloroplast stroma|GO:0009570|GR_REF:62|ISS

Also we need to add GO terms 
Fatty acid desaurase 
and 
add "stearoyl ACP desaturase" as synonym for acyl-[acyl-carrier-protein]
desaturase; GO:0045300

Thanks
Pankaj

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************




From tberardi at acoma.Stanford.EDU  Fri Jun 14 12:39:36 2002
From: tberardi at acoma.Stanford.EDU (Tanya Berardini)
Date: Fri, 14 Jun 2002 09:39:36 -0700 (PDT)
Subject: Help on curation of STAD_ORYSA
In-Reply-To: <3D0A0CE3.60C18D8F@cornell.edu>
Message-ID: <Pine.GSO.4.44.0206140911400.29687-100000@acoma.Stanford.EDU>

Pankaj,


On Fri, 14 Jun 2002, Pankaj Jaiswal wrote:

> I am confused on how to curate a rice entry which has a similarity to
> Arabidopsis protein
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=genbank&term=%22AF395441%22
>
> Which biological process should I include for
> activator signal for Jasmonic acid dependent defence response
>
> In Arabidopsis, the enzyme catalyzes a desaturation step that is required for
> Jasmonic acid biosynthesis. Also acts as an activator signal for Jasmonic acid
> dependent defence response at the time of pathogen interaction

> Annotation for rice entry
> http://www.gramene.org/perl/protein_search?protein_id=78051
>
> I have discarded the electronic annotation from Interpro matches.
>
> Molecular Function|acyl-[acyl-carrier-protein]
> desaturase|GO:0045300|GR_REF:62|ISS
> Biological Process|fatty acid elongation, unsaturated fatty
> acid|GO:0019368|GR_REF:62|ISS
> Cellular Component|plastid stroma|GO:0009532|GR_REF:62|ISS
> Cellular Component|chloroplast stroma|GO:0009570|GR_REF:62|ISS

The ISS annotations relating to the desaturase activity for function,
location, and biological process are fine. I would _not_ annotate to a
very specific biological process for the defense response related terms as
these are functions that have been described in Arabidopsis not rice.

The information below might help you in future annotations:

>From the GO documentation page:

http://www.geneontology.org/doc/GO.evidence.html

ISS inferred from sequence or structural similarity
        Sequence similarity (homologue of/most closely related to)
        Recognized domains
        Structural similarity
        Southern blotting
    Comment: Use this code for BLAST (or other sequence similarity
detection method) results that have been reviewed for accuracy by a
curator. If the result has not been reviewed, use IEA. ISS can also be
used for sequence similarities reported in published papers, if the
curator thinks the result is reliable enough.

**When the gene is a "homologue of," can infer fairly detailed function
and location (cellular component) but err on the side of low resolution
for processes.

For recognized domains, attribution to any of the ontologies will probably
be at low resolution.

    We recommend making an entry in the "with" column when using this
evidence code (i.e. include an identifier for the similar sequence).


> Also we need to add GO terms
> Fatty acid desaurase
> and
> add "stearoyl ACP desaturase" as synonym for acyl-[acyl-carrier-protein]
> desaturase; GO:0045300


fatty acid desaturase is in the GO as a synonym for stearoyl-CoA
desaturase GO:0004768, they share the same EC number 1.14.19.1
(was EC 1.14.99.5)

I looked up EC 1.14.19.2 and the synonyms for acyl-[acyl-carrier proteii]
desaturase that I found were: stearyl acyl carrier protein desaturase and
stearyl-ACP desaturase.  These can be added without any problem.

Hope this helps,

Tanya


-------------------------------------------------------------------------------
Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Fri Jun 14 12:00:09 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 14 Jun 2002 12:00:09 -0400
Subject: acyl-[acyl-carrier-protein] desaturase
References: <3D0A110D.D21725EC@cornell.edu>
Message-ID: <3D0A1309.110EA086@cornell.edu>

Hi,

I suggest correction to the EC number for  the term

acyl-[acyl-carrier-protein] desaturase 

acyl-[acyl-carrier-protein] desaturase formerly EC:1.14.99.6 is given a new EC
number 1.14.19.2

In the EC database transferred entry: now EC 1.14.19.2,
acyl-[acyl-carrier-protein] desaturase

[EC 1.14.99.6 created 1972, modified 2000, deleted 2000]


More info for EC 1.14.19.2 or EC:1.14.99.6 at
http://www.chem.qmw.ac.uk/iubmb/enzyme/EC1/14/99/6.html
http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/19/2.html


Also all the terms in CPGN should now be mapped to the Gene ontology terms for a
better corespondance.

Thanks
Pankaj


******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From pj37 at cornell.edu  Fri Jun 14 11:51:41 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 14 Jun 2002 11:51:41 -0400
Subject: Links to  Cornell (CBCG) -Plant Gene nomenclature
Message-ID: <3D0A110D.D21725EC@cornell.edu>

Hi,

On your site http://mbclserver.rutgers.edu/CPGN/
links directing to  Cornell (CBCG) don't work
Could you please correct this problem.

Thanks
Pankaj

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   
http://www.gramene.org   
******************************************


From erikesk at yahoo.com  Tue Jun 18 08:20:55 2002
From: erikesk at yahoo.com (=?iso-8859-1?q?Erike=20Widyasari?=)
Date: Tue, 18 Jun 2002 13:20:55 +0100 (BST)
Subject: Request of information about alpha-endotoxin and  gamma-endotoxin {important]
Message-ID: <20020618122055.81738.qmail@web11708.mail.yahoo.com>

Dear Dr. Y.L. Fan and or Dr. H. Yang,

I would like intropduce myself. My name is Erike
Widyasari from Indonesia.  I am studying as research
student in Nara institute of Science and Technology,
Japan.

I am interest with your paper which exposed in
yahoo.com about transgenic rice plants contained
alpha-endotoxin, and another paper about transgenic
rice plants contained gamma endotoxin.  
If you don't mind, could you please explaining about
characteristic of alpha and gamma endotoxin.  HOnestly
I still confused, since I only undertand about
delta-endotoxin of Bacillus thuringiensis.
Is it means the alpha-endotoxin and gamma -endotoxin
from the same group?
How the classification these endotoxin?
I asked about these matter because my Sensei asked me
about the classification of endotoxin.
Thank you very much for your attention.

Sincerely yours,
Erike W

__________________________________________________
Do You Yahoo!?
Yahoo! - Official partner of 2002 FIFA World Cup
http://fifaworldcup.yahoo.com


From zhang2y at tdna.es.dupont.com  Mon Jun 17 17:13:13 2002
From: zhang2y at tdna.es.dupont.com (Ying Zhang)
Date: Mon, 17 Jun 2002 17:13:13 -0400
Subject: contig_landmarkMarker
Message-ID: <3D0E50E9.BE5C9F21@tdna.es.dupont.com>

In your release of gramene 5.0, what is the difference between table
contig_landmarkMarker and contig_landmarkMarker1? According to the table
definition, they look identical except for the indexes. Thanks for any
explaination.

Ying





From schmidt at cshl.edu  Tue Jun 18 14:45:21 2002
From: schmidt at cshl.edu (Steven Schmidt)
Date: Tue, 18 Jun 2002 14:45:21 -0400
Subject: contig_landmarkMarker
In-Reply-To: <3D0E50E9.BE5C9F21@tdna.es.dupont.com>
References: <3D0E50E9.BE5C9F21@tdna.es.dupont.com>
Message-ID: <200206181845.OAA27075@cshl.org>

Hi Ying,

The schema was taken from EnsEMBL 1.0.0.
We don't use those tables.

-Steve


On Monday 17 June 2002 17:13, Ying Zhang wrote:
> In your release of gramene 5.0, what is the difference between table
> contig_landmarkMarker and contig_landmarkMarker1? According to the table
> definition, they look identical except for the indexes. Thanks for any
> explaination.
>
> Ying

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


From tbanks at agr.gc.ca  Tue Jun 18 12:53:52 2002
From: tbanks at agr.gc.ca (Travis Banks)
Date: Tue, 18 Jun 2002 12:53:52 -0400
Subject: positions of rice bacs in the genome
Message-ID: <sd0f2d72.009@em.agr.ca>

Hi,

We have an in-house genome viewer that we would like to use to visualize wheat ESTs against the rice genome (similar to what one  can do on your website).  I was wondering where if you had any files containing all of the bacs that comprise the rice chromosomes you use for your rice genome viewer, and if you have a table of relative map positions (ordering) of where the bacs lay along the chromosomes.  Thank you

Travis Banks
Molecular Bioinformaticist
Cereal Research Centre
Agriculture and Agri-Food Canada
(204) 984-2179



From pan at stein.cshl.org  Tue Jun 18 11:43:20 2002
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Tue, 18 Jun 2002 11:43:20 -0400 (EDT)
Subject: contig_landmarkMarker
In-Reply-To: <3D0E50E9.BE5C9F21@tdna.es.dupont.com>
Message-ID: <Pine.GSO.4.05.10206181131050.657-100000@phage.cshl.org>


     These two tables are actually not used in Gramene Oracle database. I
just tried to use them at the very beginning but did work for us. Now,
we created a new table named marker_clone to replace them. Please ignore
the two tables.

     I am sorry I did not remove them before publishing the schema and
data.

     Xiaokang Pan


On Mon, 17 Jun 2002, Ying Zhang wrote:

> In your release of gramene 5.0, what is the difference between table
> contig_landmarkMarker and contig_landmarkMarker1? According to the table
> definition, they look identical except for the indexes. Thanks for any
> explaination.
> 
> Ying
> 
> 
> 
> 



From rnsarma at aau.ac.in  Wed Jun 19 09:19:16 2002
From: rnsarma at aau.ac.in (R. N. Sarma)
Date: Wed, 19 Jun 2002 09:19:16 IST
Subject: ISSR marker
Message-ID: <AAUMail - 10244585563d0fff3c8d40c@intranet.aau.ac.in>

Hello,
I want to use ISSR marker in my mapping work in rice. I would like to request netter to inform me the sequences of ISSR marker of rice with their map positions and PCR profiles.

RN Sarma


From srm4 at cornell.edu  Tue Jun 18 20:34:32 2002
From: srm4 at cornell.edu (Susan McCouch)
Date: Tue, 18 Jun 2002 20:34:32 -0400
Subject: Request of information about alpha-endotoxin and 
 gamma-endotoxin {important]
In-Reply-To: <20020618122055.81738.qmail@web11708.mail.yahoo.com>
References: <20020618122055.81738.qmail@web11708.mail.yahoo.com>
Message-ID: <p05100304b93581e559dd@[128.253.184.76]>

Dear Erike,

This e-mail has come to the wrong person.  I don't know anything 
about this transgenic rice.

I hope you find the correct address for Dr. Fan and Dr. Yang.

Regards.



>Dear Dr. Y.L. Fan and or Dr. H. Yang,
>
>I would like intropduce myself. My name is Erike
>Widyasari from Indonesia.  I am studying as research
>student in Nara institute of Science and Technology,
>Japan.
>
>I am interest with your paper which exposed in
>yahoo.com about transgenic rice plants contained
>alpha-endotoxin, and another paper about transgenic
>rice plants contained gamma endotoxin. 
>If you don't mind, could you please explaining about
>characteristic of alpha and gamma endotoxin.  HOnestly
>I still confused, since I only undertand about
>delta-endotoxin of Bacillus thuringiensis.
>Is it means the alpha-endotoxin and gamma -endotoxin
>from the same group?
>How the classification these endotoxin?
>I asked about these matter because my Sensei asked me
>about the classification of endotoxin.
>Thank you very much for your attention.
>
>Sincerely yours,
>Erike W
>
>__________________________________________________
>Do You Yahoo!?
>Yahoo! - Official partner of 2002 FIFA World Cup
>http://fifaworldcup.yahoo.com


-- 
******************************************
Susan McCouch
Dept of Plant Breeding
418 Bradfield Hall
Cornell University
Ithaca, NY  14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu

******************************************


From teytelma at stein.cshl.org  Tue Jun 18 16:53:06 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Tue, 18 Jun 2002 16:53:06 -0400 (EDT)
Subject: positions of rice bacs in the genome
In-Reply-To: <sd0f2d72.009@em.agr.ca>
Message-ID: <Pine.GSO.4.05.10206181649440.12063-100000@phage.cshl.org>

Dear Mr. Banks,

Our genome browser displays the rice clones one-by-one at this point.  No
pseudomolecule for rice has been released so far, so we do not have
chromosome positions for the BACs/PACs.

Sincerely,

Lenny Teytelman

> Hi,
> 
> We have an in-house genome viewer that we would like to use to visualize wheat ESTs against the rice genome (similar to what one  can do on your website).  I was wondering where if you had any files containing all of the bacs that comprise the rice chromosomes you use for your rice genome viewer, and if you have a table of relative map positions (ordering) of where the bacs lay along the chromosomes.  Thank you
> 
> Travis Banks
> Molecular Bioinformaticist
> Cereal Research Centre
> Agriculture and Agri-Food Canada
> (204) 984-2179
> 
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From teytelma at stein.cshl.org  Tue Jun 18 16:53:06 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Tue, 18 Jun 2002 16:53:06 -0400 (EDT)
Subject: positions of rice bacs in the genome
In-Reply-To: <sd0f2d72.009@em.agr.ca>
Message-ID: <Pine.GSO.4.05.10206181649440.12063-100000@phage.cshl.org>

Dear Mr. Banks,

Our genome browser displays the rice clones one-by-one at this point.  No
pseudomolecule for rice has been released so far, so we do not have
chromosome positions for the BACs/PACs.

Sincerely,

Lenny Teytelman

> Hi,
> 
> We have an in-house genome viewer that we would like to use to visualize wheat ESTs against the rice genome (similar to what one  can do on your website).  I was wondering where if you had any files containing all of the bacs that comprise the rice chromosomes you use for your rice genome viewer, and if you have a table of relative map positions (ordering) of where the bacs lay along the chromosomes.  Thank you
> 
> Travis Banks
> Molecular Bioinformaticist
> Cereal Research Centre
> Agriculture and Agri-Food Canada
> (204) 984-2179
> 
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From lamblin at mail.ahc.umn.edu  Tue Jun 18 16:51:08 2002
From: lamblin at mail.ahc.umn.edu (Anne Lamblin (CCGB))
Date: Tue, 18 Jun 2002 15:51:08 -0500
Subject: SSRIT source code location
Message-ID: <3D0F9D3C.21CE8A25@ccgb.umn.edu>

hi Genevieve,

I am at http://www.gramene.org/gramene/searches/ssrtool

I am not able to access the location for the ssr.pl source code.
Could you please tell me the new location of the code for download?
Thanks!

Anne-Francoise

____________________________________________________
Anne-Francoise Lamblin, Ph.D.
Center for Computational Genomics and Bioinformatics
University of Minnesota
MMC43
420 Delaware Street S.E.
Minneapolis, MN 55455

Tel. (612)624-4423
Fax  (612)626-6069
lamblin at ccgb.umn.edu


From schmidt at cshl.edu  Wed Jun 19 15:28:12 2002
From: schmidt at cshl.edu (Steven Schmidt)
Date: Wed, 19 Jun 2002 15:28:12 -0400
Subject: SSRIT source code location
In-Reply-To: <3D0F9D3C.21CE8A25@ccgb.umn.edu>
References: <3D0F9D3C.21CE8A25@ccgb.umn.edu>
Message-ID: <200206191928.PAA04818@cshl.org>

Hi Anne,-Francoise,

It's at
ftp://www.gramene.org/pub/gramene/software/scripts/ssr.pl

Sorry I didn't fix the link when I moved it.

-Steve

On Tuesday 18 June 2002 16:51, Anne Lamblin (CCGB) wrote:
> hi Genevieve,
>
> I am at http://www.gramene.org/gramene/searches/ssrtool
>
> I am not able to access the location for the ssr.pl source code.
> Could you please tell me the new location of the code for download?
> Thanks!
>
> Anne-Francoise
>
> ____________________________________________________
> Anne-Francoise Lamblin, Ph.D.
> Center for Computational Genomics and Bioinformatics
> University of Minnesota
> MMC43
> 420 Delaware Street S.E.
> Minneapolis, MN 55455
>
> Tel. (612)624-4423
> Fax  (612)626-6069
> lamblin at ccgb.umn.edu

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


From teytelma at stein.cshl.org  Wed Jun 19 15:55:52 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Wed, 19 Jun 2002 15:55:52 -0400 (EDT)
Subject: SSRIT source code location
In-Reply-To: <3D0F9D3C.21CE8A25@ccgb.umn.edu>
Message-ID: <Pine.GSO.4.05.10206191553060.28476-100000@phage.cshl.org>

Dear Anne-Francoise,

I just checked the link from the ssrtool page, and it seems to work.
Could you please give me a bit more information on the error that you are
getting?

The location of the script is:
ftp://www.gramene.org/pub/gramene/software/scripts/ssr.pl

Lenny

 > hi Genevieve,
> 
> I am at http://www.gramene.org/gramene/searches/ssrtool
> 
> I am not able to access the location for the ssr.pl source code.
> Could you please tell me the new location of the code for download?
> Thanks!
> 
> Anne-Francoise
> 
> ____________________________________________________
> Anne-Francoise Lamblin, Ph.D.
> Center for Computational Genomics and Bioinformatics
> University of Minnesota
> MMC43
> 420 Delaware Street S.E.
> Minneapolis, MN 55455
> 
> Tel. (612)624-4423
> Fax  (612)626-6069
> lamblin at ccgb.umn.edu
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From teytelma at stein.cshl.org  Wed Jun 19 15:55:52 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Wed, 19 Jun 2002 15:55:52 -0400 (EDT)
Subject: SSRIT source code location
In-Reply-To: <3D0F9D3C.21CE8A25@ccgb.umn.edu>
Message-ID: <Pine.GSO.4.05.10206191553060.28476-100000@phage.cshl.org>

Dear Anne-Francoise,

I just checked the link from the ssrtool page, and it seems to work.
Could you please give me a bit more information on the error that you are
getting?

The location of the script is:
ftp://www.gramene.org/pub/gramene/software/scripts/ssr.pl

Lenny

 > hi Genevieve,
> 
> I am at http://www.gramene.org/gramene/searches/ssrtool
> 
> I am not able to access the location for the ssr.pl source code.
> Could you please tell me the new location of the code for download?
> Thanks!
> 
> Anne-Francoise
> 
> ____________________________________________________
> Anne-Francoise Lamblin, Ph.D.
> Center for Computational Genomics and Bioinformatics
> University of Minnesota
> MMC43
> 420 Delaware Street S.E.
> Minneapolis, MN 55455
> 
> Tel. (612)624-4423
> Fax  (612)626-6069
> lamblin at ccgb.umn.edu
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From noelyap at ascus.plbr.cornell.edu  Mon Jun 24 14:10:38 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Mon, 24 Jun 2002 14:10:38 -0400
Subject: ISSR marker
Message-ID: <20020624181038.GE9166@ascus.plbr.cornell.edu>

On Wed, Jun 19, 2002 at 09:19:16AM +0200, R. N. Sarma wrote:
> Hello,
> I want to use ISSR marker in my mapping work in rice. I would like
> to request netter to inform me the sequences of ISSR marker of rice
> with their map positions and PCR profiles.
> 
> RN Sarma

Dr Sarma,

You can download a file with all of the desired information at URL:

    http://www.gramene.org/microsat/microsats.txt

This is a tab-delimited file that you can load into a spreadsheet
program such as Excel.

SSR maps for rice are browsable at URL:

    http://www.gramene.org/maps/viewer?reference_map_study_id=3

Each chromosome is selectable from the "Ref. Map" drop-down list.

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From pj37 at cornell.edu  Mon Jun 24 17:20:51 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 24 Jun 2002 17:20:51 -0400
Subject: Cultivars nomenclature
Message-ID: <3D178D33.C5A69557@cornell.edu>


Dear Graham,

I was wondering, if there is an existing way of writing/representing the rice
cultivar name. I have seen people recording them in different ways like

AKITAKOMACHI -all caps
Akitakomochi -Sentence case
TAICHUNG-67
Taichung-67
Taichung 67 digits separated by space
Taichung67 digits separated by hyphen
Guang Lu Ai (IRIS version)
Guanluai (is it correct to have this)
Sometimes people are giving wrong (by our version) spellings like 
ILPOOM instead of ILPUM.
TAINONG for TAINUNG

I am not so sure about which is correct (check the capital letter within the
word)
YuNxi 2 or Yuxi 2 
WasetoiTTu or WasetoiTu 
NaCkdong or Nakdong
NoHrin or Norin  (I know there is a cultivar called "Norin", does "Nohrin"
exist)

Is there a remedy for this or should IRIS put up a nomenclature document on its
website and also a list of cultivars (searcheable) for recommended use of name.

Thanks

Pankaj



******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From pj37 at cornell.edu  Tue Jun 25 09:48:22 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 25 Jun 2002 09:48:22 -0400
Subject: Cultivars nomenclature
References: <3D178D33.C5A69557@cornell.edu>
Message-ID: <3D1874A6.AAEEC840@cornell.edu>

From:"McLaren, Graham" <G.MCLAREN at CGIAR.ORG>
Subject:RE: Cultivars nomenclature
To:"'Pankaj Jaiswal'" <pj37 at cornell.edu>

Pankaj,
You are right it is a big problem and there are no universal standards
especially when dealing with names from non alphabetic languages. What we
try to do in IRIS is accomodate all variants as alternative names with the
exception of names differing in case only - we store all names in upper
case. Then we try to identify a preferred name which will be the one used by
preference by IRIS, and we also always add a standardized name which may or
may not be the preferred name. The standardized name is derived by applying
a series of standardizations to a given name. The standardizations are not
chosen to make the name a pretty or compact as possible, but rather to
channel as may variants as possible to the same result. At present the
following standardizations are applied:

 (L= any letter; ^= space; N= any numeral, S= any of {-,',[,],+,.})
a)      Capitalize all letters                  Khao-Dawk-Mali105 becomes
KHAO-DAWK-MALI105
b)      L( becomes L^( and )L becomes )^L       IR64(BPH) becomes IR64 (BPH)
c)      N( becomes N^( and )N becomes )^N       IR64(5A) becomes IR64 (5A)
d)      L. becomes L^                           IR 63 SEL. becomes IR 64 SEL
e)      LN becomes L^N EXCEPT SLN               MALI105 becomes MALI 105 but
MALI-F4 IS unchanged
f)      NL becomes N^L EXCEPT SNL               B 533A-1 becomes B 533 A-1
but B 533 A-4B is unchanged
g)      LL-LL becomes LL^LL                     KHAO-DAWK-MALI 105 becomes
KHAO DAWK MALI 105
h)      ^0N becomes ^N                          IRTP 00123 becomes IRTP 123
i)      ^^ becomes ^                            Double spaces changed to
single spaces
j)      REMOVE LEADING OR TRAILING ^
k.      ^) becomes ) and (^ becomes (           Close in braces
l.      L-N becomes L^N when there is only one '-' in the name and L is not
preceded by a space
m.      ^/ becomes / and /^ becomes /           Close in crossing symbols

When we search the database we always search for the name as typed, with the
above standardizations applied to the input string, and to the input string
with all spaces removed. This generally catches most variants.

Hope this helps,
Graham

Pankaj Jaiswal wrote:
> 
> Dear Graham,
> 
> I was wondering, if there is an existing way of writing/representing the rice
> cultivar name. I have seen people recording them in different ways like
> 
> AKITAKOMACHI -all caps
> Akitakomochi -Sentence case
> TAICHUNG-67
> Taichung-67
> Taichung 67 digits separated by space
> Taichung67 digits separated by hyphen
> Guang Lu Ai (IRIS version)
> Guanluai (is it correct to have this)
> Sometimes people are giving wrong (by our version) spellings like
> ILPOOM instead of ILPUM.
> TAINONG for TAINUNG
> 
> I am not so sure about which is correct (check the capital letter within the
> word)
> YuNxi 2 or Yuxi 2
> WasetoiTTu or WasetoiTu
> NaCkdong or Nakdong
> NoHrin or Norin  (I know there is a cultivar called "Norin", does "Nohrin"
> exist)
> 
> Is there a remedy for this or should IRIS put up a nomenclature document on its
> website and also a list of cultivars (searcheable) for recommended use of name.
> 
> Thanks
> 
> Pankaj
> 
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
> 
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org
> ******************************************

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From marifs at hotmail.com  Tue Jun 25 14:12:37 2002
From: marifs at hotmail.com (Muhammad Arif Arif)
Date: Tue, 25 Jun 2002 18:12:37 +0000
Subject: No subject
Message-ID: <F10g41UjdSkleUBUhr3000107fb@hotmail.com>


Dear SIr/Madam
    I am working on rice in National Institute of Biotechnology and Genetic 
Engineering (NIBGE), Faisalabad, Pakistan. I want to use the SSR markers for 
rice. Kinldy let me know if i could request you for the SSR. If you supply 
the SSR markers then what is the unit price. Hope for the reply from your 
side.
Muhammad Arif


_________________________________________________________________
MSN Photos is the easiest way to share and print your photos: 
http://photos.msn.com/support/worldwide.aspx



From pj37 at cornell.edu  Tue Jun 25 09:57:10 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 25 Jun 2002 09:57:10 -0400
Subject: Cultivars nomenclature
References: <3EA5C75212CDD511B74100508BE095760122EF8D@mail.irri.cgiar.org>
Message-ID: <3D1876B6.947656A9@cornell.edu>

Dear Graham,

Thanks for the detailed information. I will adopt the same in Gramene, thus
making it easier for linking back to IRIS.

Regards
Pankaj

"McLaren, Graham" wrote:
> 
> Pankaj,
> You are right it is a big problem and there are no universal standards
> especially when dealing with names from non alphabetic languages. What we
> try to do in IRIS is accomodate all variants as alternative names with the
> exception of names differing in case only - we store all names in upper
> case. Then we try to identify a preferred name which will be the one used by
> preference by IRIS, and we also always add a standardized name which may or
> may not be the preferred name. The standardized name is derived by applying
> a series of standardizations to a given name. The standardizations are not
> chosen to make the name a pretty or compact as possible, but rather to
> channel as may variants as possible to the same result. At present the
> following standardizations are applied:
> 
>  (L= any letter; ^= space; N= any numeral, S= any of {-,',[,],+,.})
> a)      Capitalize all letters                  Khao-Dawk-Mali105 becomes
> KHAO-DAWK-MALI105
> b)      L( becomes L^( and )L becomes )^L       IR64(BPH) becomes IR64 (BPH)
> c)      N( becomes N^( and )N becomes )^N       IR64(5A) becomes IR64 (5A)
> d)      L. becomes L^                           IR 63 SEL. becomes IR 64 SEL
> e)      LN becomes L^N EXCEPT SLN               MALI105 becomes MALI 105 but
> MALI-F4 IS unchanged
> f)      NL becomes N^L EXCEPT SNL               B 533A-1 becomes B 533 A-1
> but B 533 A-4B is unchanged
> g)      LL-LL becomes LL^LL                     KHAO-DAWK-MALI 105 becomes
> KHAO DAWK MALI 105
> h)      ^0N becomes ^N                          IRTP 00123 becomes IRTP 123
> i)      ^^ becomes ^                            Double spaces changed to
> single spaces
> j)      REMOVE LEADING OR TRAILING ^
> k.      ^) becomes ) and (^ becomes (           Close in braces
> l.      L-N becomes L^N when there is only one '-' in the name and L is not
> preceded by a space
> m.      ^/ becomes / and /^ becomes /           Close in crossing symbols
> 
> When we search the database we always search for the name as typed, with the
> above standardizations applied to the input string, and to the input string
> with all spaces removed. This generally catches most variants.
> 
> Hope this helps,
> Graham
> 
> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Tuesday, June 25, 2002 5:21 AM
> To: Graham Mclaren; Susan McCouch; Doreen Ware; Richard Bruskiewich;
> brie
> Subject: Cultivars nomenclature
> 
> Dear Graham,
> 
> I was wondering, if there is an existing way of writing/representing the
> rice
> cultivar name. I have seen people recording them in different ways like
> 
> AKITAKOMACHI -all caps
> Akitakomochi -Sentence case
> TAICHUNG-67
> Taichung-67
> Taichung 67 digits separated by space
> Taichung67 digits separated by hyphen
> Guang Lu Ai (IRIS version)
> Guanluai (is it correct to have this)
> Sometimes people are giving wrong (by our version) spellings like
> ILPOOM instead of ILPUM.
> TAINONG for TAINUNG
> 
> I am not so sure about which is correct (check the capital letter within the
> word)
> YuNxi 2 or Yuxi 2
> WasetoiTTu or WasetoiTu
> NaCkdong or Nakdong
> NoHrin or Norin  (I know there is a cultivar called "Norin", does "Nohrin"
> exist)
> 
> Is there a remedy for this or should IRIS put up a nomenclature document on
> its
> website and also a list of cultivars (searcheable) for recommended use of
> name.
> 
> Thanks
> 
> Pankaj
> 
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
> 
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org
> ******************************************

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From Bdmanager at alba-lux.com  Wed Jun 26 14:38:45 2002
From: Bdmanager at alba-lux.com (Barbara Thomas)
Date: Wed, 26 Jun 2002 20:38:45 +0200
Subject: Alba Lux cooperation proposal
Message-ID: <200206261844.OAA08662@stein.cshl.org>

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From jde22 at cornell.edu  Thu Jun 27 16:09:52 2002
From: jde22 at cornell.edu (jde22 at cornell.edu)
Date: Thu, 27 Jun 2002 16:09:52 -0400 (EDT)
Subject: obtaining sequences
Message-ID: <Pine.SOL.3.91.1020627153223.8617A-100000@travelers.mail.cornell.edu>

I have an idea for Gramene that I think will be very useful for many 
users.  It would be great if there was a way to download specific 
pieces of sequences by submitting a list of BACs 
(or any other sequences) and regions within those sequences.  So, the 
user would specify the BAC and the beginning and end of the sequences of 
interest and the sequences would be returned, perhaps in FASTA format.  This is 
something that Genbank should do, but doesn't, and most of us spend too 
much time cutting out the sequences that we want.  A batch option would 
also be really great.  I typically write scripts and have a few other 
tricks to do this, but for the typical user, it is a real chore. 

Jeremy Edwards


From noelyap at ascus.plbr.cornell.edu  Wed Jun 26 14:53:37 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Wed, 26 Jun 2002 14:53:37 -0400
Subject: SSR primers
In-Reply-To: <F10g41UjdSkleUBUhr3000107fb@hotmail.com>
References: <F10g41UjdSkleUBUhr3000107fb@hotmail.com>
Message-ID: <20020626185337.GA13835@ascus.plbr.cornell.edu>

On Tue, Jun 25, 2002 at 06:12:37PM +0000, Muhammad Arif Arif wrote:
> 
> Dear SIr/Madam
>    I am working on rice in National Institute of Biotechnology and Genetic 
> Engineering (NIBGE), Faisalabad, Pakistan. I want to use the SSR markers 
> for rice. Kinldy let me know if i could request you for the SSR. If you 
> supply the SSR markers then what is the unit price. Hope for the reply from 
> your side.

We do not provide rice markers, but the SSR primers are available
commercially from Research Genetics (now a part of Invitrogen).  Go to
their website at:

    http://www.invitrogen.com

Do a search on "mappairs".  This will return links to several PDF
files.  Click on the first one to get a brochure that explains how to
you can order primers.  

You can also email info at resgen.com
The rice primers are called "ResGen MapPairs Rice cDNA Library Markers".

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From pj37 at cornell.edu  Thu Jun 27 17:34:11 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 27 Jun 2002 17:34:11 -0400
Subject: [Fwd: Ontology Submission from gramene.org]
Message-ID: <3D1B84D3.D9836466@cornell.edu>

Dear Shashidhar,

Thank you very much for your suggestion. 

We have reframed the definition of Trait Ontology term: harvesting index
(TO:0000128) to :
"proportion of usable (economically significant) biomass over total (biological)
biomass, expressed as a percentage."

Also the term name will be changed to  "harvest index" (TO:0000128) instead of
"harvesting index"

The changes will appear in our next release of Gramene database.

Sincerely

Pankaj

ontology_submission at brie.cshl.org wrote:
> 
> plant_type      plant_type_other        state   suggested_term  telephone       comments        address first_name      definition      reference_category      submission_type email_address   postal_code     reference_curator       relationship_to_parent1 submission_type_other   relationship_to_parent2 parent_term1    parent_term2    reference_details       last_name       country organization    middle_initial  city    parent1_go_po_id        associated_ontology     parent2_go_po_id        synonym reference_source        fax
> ""      ""      ""      "Harvest Index" "91-80 3636201" ""      "GKVK, "        "Halagappa"     "Harvest Index is abbreviated as HI.  It is the proportion of economic yield to Biological yield, on dry weight basis and expressed as percentage.   "  "Published"     "Correction"    "heshashidhar at rediffmail.com"   "560065"        ""      ""      "Harvesting Index"      ""      ""      "Shashidhar"    "India" "University of Agricultural Sciences"   "E"     "Bangalore"     ""      "TO: Trait Ontology"    ""      ""      ""      "91-80 3330153"

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From shenoyvv at sify.com  Thu Jun 27 23:40:36 2002
From: shenoyvv at sify.com (SHENOY VV)
Date: Fri, 28 Jun 2002 09:10:36 +0530
Subject: Primers for RG and RZ clones
Message-ID: <001201c21e55$96830ea0$dcd9d6d2@computer4>

Hello,

I am looking for STS-primer sequences for the RG and RZ clones that have been published. 

Can anyone kindly help me by informing where on the net this information is available in downloadable format?

Thanks.

Shenoy
28.6.2002
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From lstein at stein.cshl.org  Fri Jun 28 11:42:07 2002
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Fri, 28 Jun 2002 11:42:07 -0400
Subject: obtaining sequences
In-Reply-To: <Pine.SOL.3.91.1020627153223.8617A-100000@travelers.mail.cornell.edu>
References: <Pine.SOL.3.91.1020627153223.8617A-100000@travelers.mail.cornell.edu>
Message-ID: <200206281142.07776.lstein@cshl.org>

I support this idea.

Lincoln

On Thursday 27 June 2002 04:09 pm, jde22 at cornell.edu wrote:
> I have an idea for Gramene that I think will be very useful for many
> users.  It would be great if there was a way to download specific
> pieces of sequences by submitting a list of BACs
> (or any other sequences) and regions within those sequences.  So, the
> user would specify the BAC and the beginning and end of the sequences of
> interest and the sequences would be returned, perhaps in FASTA format. 
> This is something that Genbank should do, but doesn't, and most of us spend
> too much time cutting out the sequences that we want.  A batch option would
> also be really great.  I typically write scripts and have a few other
> tricks to do this, but for the typical user, it is a real chore.
>
> Jeremy Edwards

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


From noelyap at ascus.plbr.cornell.edu  Fri Jun 28 11:03:37 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Fri, 28 Jun 2002 11:03:37 -0400
Subject: Gramene comparative maps (WAS: Re: [Fwd: Ontology Submission from gramene.org])
In-Reply-To: <3D1C7388.C5AF0958@cornell.edu>
References: <20020628115810.9295.qmail@webmail28.rediffmail.com> <3D1C7388.C5AF0958@cornell.edu>
Message-ID: <20020628150337.GA28709@ascus.plbr.cornell.edu>

On Fri, Jun 28, 2002 at 10:32:40AM -0400, Pankaj Jaiswal wrote:
> "H. E. Shashidhar" wrote:
> > 2.  How can I compare the different rice maps with reference to
> > relative position of markers.  I say a presentation by Robert (of
> > IRRI Biometrics division recently in a workshop in Philippines).
> > Does Gramine support such a tool?
> > 
> 
> I will ask our comparative map curator, Noel Yap to specifically answer this
> query.

You can compare two maps using the Gramene Map Viewer:

    http://www.gramene.org/maps/viewer

First, select a mapping study from the "Ref. Study" drop-down, then
select a linkage group from the "Ref. Map".  This will show you the
linkage map for that one study.  For example, you can see chromosome 1
from the Japanese RFLP map:

    http://www.gramene.org/maps/viewer?reference_map_id=25&prev_reference_map_id=&reference_map_study_id=2

You can then select another map to compare to the reference map.  The
"Comp. Map" listbox shows all other maps (both physical and genetic)
in Gramene that have some correspondence with the reference map.
Select a map from the list and click on the "Show map" button.  For
example, you can compare chromosome 1 from the Japanese map with the
corresponding chromsome from the Cornell RFLP map:

    http://www.gramene.org/maps/viewer?start=0&end=181.8&highlight=&comparative_map1=genetic_map_id%3D1&show_only_concordant_contigs=1&image_height=400&font_size=small&image_type=png&reference_map_study_id=2&reference_map_id=25&start=0&end=181.8&highlight=&flip=

We will soon have the capability to compare more than two maps at a
time.  We'll post a news item on the Gramene home page when that
happens.

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From lstein at stein.cshl.org  Fri Jun 28 11:42:07 2002
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Fri, 28 Jun 2002 11:42:07 -0400
Subject: obtaining sequences
In-Reply-To: <Pine.SOL.3.91.1020627153223.8617A-100000@travelers.mail.cornell.edu>
References: <Pine.SOL.3.91.1020627153223.8617A-100000@travelers.mail.cornell.edu>
Message-ID: <200206281142.07776.lstein@cshl.org>

I support this idea.

Lincoln

On Thursday 27 June 2002 04:09 pm, jde22 at cornell.edu wrote:
> I have an idea for Gramene that I think will be very useful for many
> users.  It would be great if there was a way to download specific
> pieces of sequences by submitting a list of BACs
> (or any other sequences) and regions within those sequences.  So, the
> user would specify the BAC and the beginning and end of the sequences of
> interest and the sequences would be returned, perhaps in FASTA format. 
> This is something that Genbank should do, but doesn't, and most of us spend
> too much time cutting out the sequences that we want.  A batch option would
> also be really great.  I typically write scripts and have a few other
> tricks to do this, but for the typical user, it is a real chore.
>
> Jeremy Edwards

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


From noelyap at ascus.plbr.cornell.edu  Fri Jun 28 11:22:24 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Fri, 28 Jun 2002 11:22:24 -0400
Subject: Primers for RG and RZ clones
In-Reply-To: <001201c21e55$96830ea0$dcd9d6d2@computer4>
References: <001201c21e55$96830ea0$dcd9d6d2@computer4>
Message-ID: <20020628152224.GB28709@ascus.plbr.cornell.edu>

On Fri, Jun 28, 2002 at 09:10:36AM +0530, SHENOY VV wrote:
> I am looking for STS-primer sequences for the RG and RZ clones that have been published. 
> 
> Can anyone kindly help me by informing where on the net this information is available in downloadable format?

Dear Shenoy,

Unfortunately, there are no publicly-available STS-primers for the RG
and RZ clones.  However, sequence is available for most of these
clones in Genbank:

    http://www.ncbi.nlm.nih.gov/

You are free to develop your own primers from these sequences.

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From pj37 at cornell.edu  Fri Jun 28 10:32:40 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 28 Jun 2002 10:32:40 -0400
Subject: [Fwd: Ontology Submission from gramene.org]
References: <20020628115810.9295.qmail@webmail28.rediffmail.com>
Message-ID: <3D1C7388.C5AF0958@cornell.edu>

Dear Shashidhar,


"H. E. Shashidhar" wrote:
> 
> Dear Pankaj,
>    Hai,  Great to know that you are part of the team
> developing/maintaining www.gramine.org.
>     I have been spending a lot of time in this site.  I have found
> it very useful for my work and teaching.  I have a few
> questions/clarifications.

Its great to learn that people are using Gramene in their research. Please feel
free to contact the Gramene team at gramene at gramene.org, your feedback is
valuable to us.

> 1.  Could you please give me the email of Edith Paul?  I have been
> trying to reach her to discuss about her software GeneFlow.  I
> cant trace her address.

Edie Paul <epaul at geneflowinc.com>

> 2.  How can I compare the different rice maps with reference to
> relative position of markers.  I say a presentation by Robert (of
> IRRI Biometrics division recently in a workshop in Philippines).
> Does Gramine support such a tool?
> 

I will ask our comparative map curator, Noel Yap to specifically answer this
query.

Best regards
Pankaj

> Best Regards
> Shashidhar, HE
> Associate Professor,
> Dept. Genetics & Plant Breeding,
> College of Agriculture, GKVK, Bangalore
> 650065, India
> On Fri, 28 Jun 2002 Pankaj Jaiswal wrote :
> >Dear Shashidhar,
> >
> >Thank you very much for your suggestion.
> >
> >We have reframed the definition of Trait Ontology term:
> >harvesting index
> >(TO:0000128) to :
> >"proportion of usable (economically significant) biomass over
> >total (biological)
> >biomass, expressed as a percentage."
> >
> >Also the term name will be changed to  "harvest index"
> >(TO:0000128) from
> >"harvesting index"
> >
> >The changes will appear in our next release of Gramene
> >database.
> >
> >Sincerely
> >
> >Pankaj
> >
> >ontology_submission at brie.cshl.org wrote:
> > >
> > > plant_type      plant_type_other        state   suggested_term
> >telephone       comments        address first_name
> >definition      reference_category      submission_type
> >email_address   postal_code     reference_curator
> >relationship_to_parent1 submission_type_other
> >relationship_to_parent2 parent_term1    parent_term2
> >reference_details       last_name       country organization
> >middle_initial  city    parent1_go_po_id
> >associated_ontology     parent2_go_po_id        synonym
> >reference_source        fax
> > > ""      ""      ""      "Harvest Index" "91-80 3636201" ""
> >"GKVK, "        "Halagappa"     "Harvest Index is abbreviated as
> >HI.  It is the proportion of economic yield to Biological yield,
> >on dry weight basis and expressed as percentage.   "  "Published"
> >"Correction"    "heshashidhar at rediffmail.com"   "560065"
> >""      ""      "Harvesting Index"      ""      ""
> >"Shashidhar"    "India" "University of Agricultural Sciences"
> >"E"     "Bangalore"     ""      "TO: Trait Ontology"    ""
> >""      ""      "91-80 3330153"
> >
> >--
> >
> >******************************************
> >Pankaj Jaiswal, Ph.D.
> >Postdoctoral Associate
> >Dept. of Plant Breeding
> >Cornell University
> >Ithaca, NY-14853, USA
> >
> >E mail: pj37 at cornell.edu
> >http://www.gramene.org
> >******************************************
> 
> _________________________________________________________
> There is always a better job for you at Monsterindia.com.
> Go now http://monsterindia.com/rediffin/

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From heshashidhar at rediffmail.com  Sat Jun 29 00:40:24 2002
From: heshashidhar at rediffmail.com (H. E. Shashidhar)
Date: 29 Jun 2002 04:40:24 -0000
Subject: Gramene comparative maps (WAS: Re: [Fwd: Ontology Submission from gramene.org])
Message-ID: <20020629044024.4684.qmail@webmail17.rediffmail.com>

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From matthews at greengenes.cit.cornell.edu  Sat Jun 29 14:50:39 2002
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Sat, 29 Jun 2002 14:50:39 -0400 (EDT)
Subject: Updated Wheat Alignments
Message-ID: <200206291850.OAA22627@greengenes.cit.cornell.edu>

Hi Lenny,

Thanks!  I've loaded these in GrainGenes as links to Gramene's BAC/PAC 
Genome Browser records, and I've updated our WhatsNew at
http://wheat.pw.usda.gov/ggpages/whatsnew/.

best,
- Dave

> From teytelma at cshl.org Fri Jun 21 00:13:59 2002
> 
> I have redone the EST alignments for wheat.  These updated alignments
> represent 71,683 ESTs, compared to the previous 24,601. 
> ...


