From pessoa at cenargen.embrapa.br  Thu Apr  3 08:39:34 2003
From: pessoa at cenargen.embrapa.br (Marco Filho)
Date: Thu, 3 Apr 2003 10:39:34 -0300 (EST)
Subject: information on contigs
Message-ID: <200304031339.h33DdYx25825@uba.cenargen.embrapa.br>

I'm having some problems interpreting the information on some 
contigs..For instance: ctg220 on rice chromosome 10 - there are three 
clones at the top with the same identification - which one should I 
regard as the most reliable? Do they all provide the same information?

And again, when I open the "feature detail" window for that clone, it 
shows 

Database Cross-References:  Not available 

..while many of other clones I looked at before this one have a link 
for "Gramene" and the EnsEMBL genome server..

Any instructions on that?

Thanks in advance..
Marco

----------------------------------------------------
Marco Aur?lio Caldas de Pinho Pessoa Filho
Universidade de Bras?lia - UnB
Embrapa/Recursos Gen?ticos e Biotecnologia
Laborat?rio de Gen?tica Vegetal - Plant Genetics Lab
Bras?lia-DF
Brasil



From teytelma at cshl.edu  Thu Apr  3 11:51:27 2003
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Thu, 3 Apr 2003 11:51:27 -0500 (EST)
Subject: information on contigs
In-Reply-To: <200304031339.h33DdYx25825@uba.cenargen.embrapa.br>
Message-ID: <Pine.GSO.4.05.10304031150390.24898-100000@phage.cshl.org>

Dear Marco,

Could you please tell me precisely what you are viewing (sending the link
is the best).  Which specific clones do you have a question about?

Thanks,

Lenny

> I'm having some problems interpreting the information on some 
> contigs..For instance: ctg220 on rice chromosome 10 - there are three 
> clones at the top with the same identification - which one should I 
> regard as the most reliable? Do they all provide the same information?
> 
> And again, when I open the "feature detail" window for that clone, it 
> shows 
> 
> Database Cross-References:  Not available 
> 
> ..while many of other clones I looked at before this one have a link 
> for "Gramene" and the EnsEMBL genome server..
> 
> Any instructions on that?
> 
> Thanks in advance..
> Marco
> 
> ----------------------------------------------------
> Marco Aur?lio Caldas de Pinho Pessoa Filho
> Universidade de Bras?lia - UnB
> Embrapa/Recursos Gen?ticos e Biotecnologia
> Laborat?rio de Gen?tica Vegetal - Plant Genetics Lab
> Bras?lia-DF
> Brasil
> 
> 

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



From pessoa at cenargen.embrapa.br  Fri Apr  4 12:32:40 2003
From: pessoa at cenargen.embrapa.br (Marco Filho)
Date: Fri, 4 Apr 2003 14:32:40 -0300 (EST)
Subject: information on contigs
Message-ID: <200304041732.h34HWec26815@uba.cenargen.embrapa.br>

Dear Lenny,

The link I mentioned is the following:(hope it works)

http://www.gramene.org/cmap/map_details?
ref_map_set_aid=imap;ref_map_aid=191;comparative_maps=-1%3dmap_aid%3d10
[57.8,70.7];label_features=all;feature_types=;highlight=RZ892

The clone is AC02340, at the top. There are three bars, so I figured 
they would contain different information. When you click on one of 
those bars, the "Feature detail" window will be opened. There you would 
usually find a link for the EnsEMBL server window, where you can browse 
through the predicted and annotated transcripts for that clone. There's 
no such link for this clone: for "Database cross-references" you'll 
see "NOT AVAILABLE"

So I wonder how I could find the link for that clone.

Thanks again,
Marco


> Dear Marco,
> 
> Could you please tell me precisely what you are viewing (sending the 
link
> is the best).  Which specific clones do you have a question about?
> 
> Thanks,
> 
> Lenny
> 

----------------------------------------------------
Marco Aur?lio Caldas de Pinho Pessoa Filho
Universidade de Bras?lia - UnB
Embrapa/Recursos Gen?ticos e Biotecnologia
Laborat?rio de Gen?tica Vegetal
Bras?lia-DF
Brasil



From schmidt at cshl.edu  Wed Apr  9 17:11:23 2003
From: schmidt at cshl.edu (Steven Schmidt)
Date: Wed, 9 Apr 2003 17:11:23 -0400
Subject: test
Message-ID: <200304091711.23105.schmidt@cshl.edu>

Testing new mailing lists which should go via brie4
-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-8892




From matthews at greengenes.cit.cornell.edu  Sat Apr 12 12:13:19 2003
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Sat, 12 Apr 2003 12:13:19 -0400 (EDT)
Subject: finding search results in Genome View
Message-ID: <200304121613.h3CGDJ4Y004653@greengenes.cit.cornell.edu>

When you search for a feature (marker C585 for example), either with BLAST
or by its name, the view of the BAC clone in Genome View always shows
the leftmost 50 kb of the clone.  Which in this example doesn't even
include the region where the feature is.  Besides which, 50 kb is a lot 
of little rectangles to mouseover trying to find the feature you were
looking for, if it isn't one that's labeled.

It would be much better if Genome View could zoom in on the item found, like
GBrowse does, cf. http://wheat.pw.usda.gov/cgi-bin/gbrowse.

- Dave


From ware at cshl.edu  Mon Apr 14 08:24:24 2003
From: ware at cshl.edu (Ware, Doreen)
Date: Mon, 14 Apr 2003 08:24:24 -0400
Subject: finding search results in Genome View
Message-ID: <39FDE54A4920D411AE0C0090274602F202D0968F@exch01.cshl.org>

Hi Dave,

I agree with you. The current version of Ensembl does not have that
flexibility for features.  The new Ensembl will though.  We hope to have the
new version up at the end of June.

Doreen


-----Original Message-----
From: Dave Matthews [mailto:matthews at greengenes.cit.cornell.edu]
Sent: Saturday, April 12, 2003 12:13 PM
To: Gramene mailgroup
Subject: finding search results in Genome View

When you search for a feature (marker C585 for example), either with BLAST
or by its name, the view of the BAC clone in Genome View always shows
the leftmost 50 kb of the clone.  Which in this example doesn't even
include the region where the feature is.  Besides which, 50 kb is a lot
of little rectangles to mouseover trying to find the feature you were
looking for, if it isn't one that's labeled.

It would be much better if Genome View could zoom in on the item found, like
GBrowse does, cf. http://wheat.pw.usda.gov/cgi-bin/gbrowse.

- Dave


From pessoa at cenargen.embrapa.br  Sat Apr 12 21:18:58 2003
From: pessoa at cenargen.embrapa.br (Marco Filho)
Date: Sat, 12 Apr 2003 22:18:58 -0300 (EST)
Subject: finding search results in Genome View
Message-ID: <200304130118.h3D1IwZ12167@uba.cenargen.embrapa.br>

I?m not sure I really understood your problem, but you can view the 
whole clone by clicking on the bottom figure (the one which shows you a 
zoom of the leftmost area of the clone. By placing your mouse on the 
bottom figure you?ll have the "contig information" option...that will 
show you the whole clone with the submitted transcripts and other 
information such as markers.

Marco

> When you search for a feature (marker C585 for example), either with 
BLAST
> or by its name, the view of the BAC clone in Genome View always shows
> the leftmost 50 kb of the clone.  Which in this example doesn't even
> include the region where the feature is.  Besides which, 50 kb is a 
lot 
> of little rectangles to mouseover trying to find the feature you were
> looking for, if it isn't one that's labeled.
> 
> It would be much better if Genome View could zoom in on the item 
found, like
> GBrowse does, cf. http://wheat.pw.usda.gov/cgi-bin/gbrowse.
> 
> - Dave
> 
> 

----------------------------------------------------
Marco Aur?lio Caldas de Pinho Pessoa Filho
Universidade de Bras?lia - UnB
Embrapa/Recursos Gen?ticos e Biotecnologia
Laborat?rio de Gen?tica Vegetal
Bras?lia-DF
Brasil



From cschen at uclink.berkeley.edu  Wed Apr 16 17:23:11 2003
From: cschen at uclink.berkeley.edu (Calvin Chen)
Date: Wed, 16 Apr 2003 14:23:11 -0700
Subject: Barley EST database
Message-ID: <000001c3045e$65b56710$5e582080@habuji01>

Hi,
 
I'm working here from UC Berkeley trying to blast some things against
the Barley EST database.  However I'm getting an error: 
 
FATAL:  Could not open the database:  Barley_EST
 
EXIT CODE 18
 
 
I was wondering if u knew what is causing the error.  Thanks for your
help.
 
Calvin Chen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030416/00775b75/attachment.html>

From teytelma at cshl.edu  Thu Apr 17 10:29:51 2003
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Thu, 17 Apr 2003 10:29:51 -0400 (EDT)
Subject: Barley EST database
In-Reply-To: <000001c3045e$65b56710$5e582080@habuji01>
Message-ID: <Pine.GSO.4.05.10304171023530.13693-100000@phage.cshl.edu>

Dear Calvin,

Apparently, BLAST did not properly create the database from the
Barley fasta file.  I am now looking into it and will rebuild the
database.

I'll email you as soon as it's up.

Thanks for notifying us.


Lenny

> Hi,
>  
> I'm working here from UC Berkeley trying to blast some things against
> the Barley EST database.  However I'm getting an error: 
>  
> FATAL:  Could not open the database:  Barley_EST
>  
> EXIT CODE 18
>  
>  
> I was wondering if u knew what is causing the error.  Thanks for your
> help.
>  
> Calvin Chen



From teytelma at cshl.edu  Thu Apr 17 16:31:05 2003
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Thu, 17 Apr 2003 16:31:05 -0400 (EDT)
Subject: Barley EST database
In-Reply-To: <000001c3045e$65b56710$5e582080@habuji01>
Message-ID: <Pine.GSO.4.05.10304171629380.13693-100000@phage.cshl.edu>

Dear Calvin,

The barley BLAST should now be fixed.

One of the Genbank sequences had multiple non-nucleotide characters, and 
WU-BLAST simply pretended to create the BLAST database. :-)

Lenny

> Hi,
>  
> I'm working here from UC Berkeley trying to blast some things against
> the Barley EST database.  However I'm getting an error: 
>  
> FATAL:  Could not open the database:  Barley_EST
>  
> EXIT CODE 18
>  
>  
> I was wondering if u knew what is causing the error.  Thanks for your
> help.
>  
> Calvin Chen
> 

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



From zhangy at genomics.org.cn  Fri Apr 18 01:47:38 2003
From: zhangy at genomics.org.cn (Yong Zhang)
Date: Fri, 18 Apr 2003 13:47:38 +0800
Subject: where can I download Rice QTLs data?
Message-ID: <015b01c3056e$0f1f3230$1e04a8c0@BGI.LOCAL>

Hi,

I am doing some research work related to rice QTLs.
How can I download the data from Gramene website? (link?)

zhangyong




From gksw at u.washington.edu  Thu Apr 17 20:37:49 2003
From: gksw at u.washington.edu (Gane Ka-Shu Wong)
Date: Thu, 17 Apr 2003 17:37:49 -0700
Subject: downloading all the mapped QTLs
Message-ID: <000801c30542$bd718620$77495f80@polymorph>

a colleague at syngenta mentioned that "gramene" (or actually it's predecessor riceGenes) had a list of all the QTLs. i could not figure out how to get this information from gramene, although i did notice under 

http://www.gramene.org/cmap/feature_search

that QTL is one of the recognized feature type. but i simply could not get it to return anything. are QTLs supported or not and, if so, where do i download a list of traits for which the mapping has already been done? 




Gane Ka-Shu Wong
Beijing Institute of Genomics
Associate Director
 
University of Washington
UW Genome Center
Fluke Hall, Mason Road
Seattle, WA 98195
 
gksw at u.washington.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030417/e3a2831a/attachment.html>

From iroja at sltnet.lk  Thu Apr 17 13:22:14 2003
From: iroja at sltnet.lk (Iroja Caldera)
Date: Thu, 17 Apr 2003 23:22:14 +0600
Subject: Query regarding citations
Message-ID: <000901c30505$e7c5ef70$71575ecb@genius>

Dear Sir/Madam,

Is the Rice Genetics Newsletter solely confined as a web document or is it published as well?
If any work from these articles are used,how should one cite the authors?

Thank you,
Iroja
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030417/08739ed7/attachment.html>

From pj37 at cornell.edu  Fri Apr 18 10:36:25 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 18 Apr 2003 10:36:25 -0400
Subject: downloading all the mapped QTLs
References: <000801c30542$bd718620$77495f80@polymorph>
Message-ID: <3EA00D69.37F7838E@cornell.edu>

Dear Dr. Wong,

My comments are as follows.

> Gane Ka-Shu Wong wrote:
> 
> a colleague at syngenta mentioned that "gramene" (or actually it's predecessor
> riceGenes) had a list of all the QTLs. i could not figure out how to get this

You are right, RiceGenes database, had the QTL info but we do not maintain that
information anymore in Gramene. However, we are working on putting together the
rice QTL data in Gramene in a new format and it should be available soon.


> information from gramene, although i did notice under
> 
> http://www.gramene.org/cmap/feature_search
> 
> that QTL is one of the recognized feature type. but i simply could not get it
> to return anything. are QTLs supported or not and, if so, where do i download
> a list of traits for which the mapping has already been done?
> 

As I said this is a work in progress and it should not have appeared on the
feature list at. 
We apologize for the inconvenience. As soon as the QTL information is made
available, we will inform you.

Sincerely,

Pankaj
www.grameme.org

> 
> 
> 
> Gane Ka-Shu Wong
> Beijing Institute of Genomics
> Associate Director
> 
> University of Washington
> UW Genome Center
> Fluke Hall, Mason Road
> Seattle, WA 98195
> 
> gksw at u.washington.edu


From pj37 at cornell.edu  Fri Apr 18 10:42:00 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 18 Apr 2003 10:42:00 -0400
Subject: where can I download Rice QTLs data?
References: <015b01c3056e$0f1f3230$1e04a8c0@BGI.LOCAL>
Message-ID: <3EA00EB8.9409047@cornell.edu>

Dear Zhang,

Putting together the rice QTL information is a work in progress at Gramene. As
soon as it is available, we will let you know.

Thanks

Pankaj
www.gramene.org


Yong Zhang wrote:
> 
> Hi,
> 
> I am doing some research work related to rice QTLs.
> How can I download the data from Gramene website? (link?)
> 
> zhangyong


From jn66 at cornell.edu  Fri Apr 18 10:57:17 2003
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Fri, 18 Apr 2003 10:57:17 -0400
Subject: Query regarding citations
References: <000901c30505$e7c5ef70$71575ecb@genius>
Message-ID: <3EA0124D.9197A50A@cornell.edu>

Dear Iroja,

RGN is published by Rice Genetics Cooperative every year with normal
hard copy version. You can cite those articles from RGN following
general format [author---year---title name---journal name
(RGN)---volume---page number].

We noticed, for the electric version displayed by Gramene, the page
number for the article is not so obvious from article page. However, you
can easily get page number for the article from table of content page.
For instance, you can find the page number for the article
(http://brie2.cshl.org:8082/newsletters/rice_genetics/rgn14/v14p57.html)

at:
http://brie2.cshl.org:8082/newsletters/rice_genetics/rgn14/table_of_contents.html

Hope this info helpful to you.

Junjian Ni
in Gramene


Iroja Caldera wrote:

> Dear Sir/Madam, Is the Rice Genetics Newsletter solely confined as a
> web document or is it published as well?If any work from these
> articles are used,how should one cite the authors? Thank you,Iroja
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20030418/00823895/attachment.html>

