From pj37 at cornell.edu  Tue Nov  1 11:04:09 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 01 Nov 2005 11:04:09 -0500
Subject: [Fwd: [Fwd: Gene Ontology Consortium survey]]
Message-ID: <436791F9.4010105@cornell.edu>


Hi Everyone,

The Gramene users that have used Gene Ontologies (GO)
(www.geneontology.org) or have been interested in this work, please take
a look at the following mail. The project needs your much appreciated
feedback.

Gramene database uses these ontologies to describe the gene or protein's 
  molecular function, role in a biological process and localization in a 
cellular component. e.g. the rice Hd3a protein 
(http://www.gramene.org/db/protein/protein_search?acc=Q93WI9) has 
annotations to many of the GO terms. These are the specific annotations, 
but if you are interested in knowing more about the 'inflorescence 
development (GO:0010229)', please click on the term name that will take 
you to the ontology pages, where you will find information on the 
definition and the lineage of the term in the ontology, in addition to 
all the other rice proteins that have been annotated for this process term.

Gramene Tip:

Using ontologies is one easy way to find all the proteins associated to 
a given biological process/function/cellular component.


Thanks
Pankaj

-------- Original Message --------
Subject: Gene Ontology Consortium survey
Date: Tue, 01 Nov 2005 14:20:10 +0000
From: J Clark <jclark at ebi.ac.uk>
Reply-To: JClark <jclark at ebi.ac.uk>
To: undisclosed-recipients:;

Hi,

The Gene Ontology Project grant is up for competitive
renewal this year. This is a really important thing for us
since the work of the GO project cannot continue if our
grant is not renewed. Conversely, if we get additional funding
  we will be able to provide greatly enhanced services and
perhaps wider annotation coverage. To help gather evidence of the
popularity of our services, to support our grant application,
we are sending out a questionnaire to our users.

Would it be possible to take 10 minutes to take part in our survey?:
http://www.AdvancedSurvey.com/default.asp?SurveyID=32355

Also if you could pass on this mail to colleagues or to any
appropriate news groups or mailing lists we'd be very grateful.

Thanks ever so much for your time.

Best wishes,

Jennifer Clark
GO Curator






-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683



From jn66 at cornell.edu  Tue Nov  1 11:17:03 2005
From: jn66 at cornell.edu (Junjian Ni)
Date: Tue, 1 Nov 2005 11:17:03 -0500 (EST)
Subject: [Fwd: [Fwd: Gene Ontology Consortium survey]]
In-Reply-To: <436791F9.4010105@cornell.edu>
References: <436791F9.4010105@cornell.edu>
Message-ID: <1463.128.253.246.144.1130861823.squirrel@webmail.cornell.edu>

Pankaj,

Looks nice to me. Thanks.

Ni
>
> Hi Everyone,
>
> The Gramene users that have used Gene Ontologies (GO)
> (www.geneontology.org) or have been interested in this work, please take
a look at the following mail. The project needs your much appreciated
feedback.
>
> Gramene database uses these ontologies to describe the gene or protein's
>   molecular function, role in a biological process and localization in a
> cellular component. e.g. the rice Hd3a protein
> (http://www.gramene.org/db/protein/protein_search?acc=Q93WI9) has
annotations to many of the GO terms. These are the specific annotations,
but if you are interested in knowing more about the 'inflorescence
development (GO:0010229)', please click on the term name that will take
you to the ontology pages, where you will find information on the
definition and the lineage of the term in the ontology, in addition to
all the other rice proteins that have been annotated for this process
term.
>
> Gramene Tip:
>
> Using ontologies is one easy way to find all the proteins associated to
a given biological process/function/cellular component.
>
>
> Thanks
> Pankaj
>
> -------- Original Message --------
> Subject: Gene Ontology Consortium survey
> Date: Tue, 01 Nov 2005 14:20:10 +0000
> From: J Clark <jclark at ebi.ac.uk>
> Reply-To: JClark <jclark at ebi.ac.uk>
> To: undisclosed-recipients:;
>
> Hi,
>
> The Gene Ontology Project grant is up for competitive
> renewal this year. This is a really important thing for us
> since the work of the GO project cannot continue if our
> grant is not renewed. Conversely, if we get additional funding
>   we will be able to provide greatly enhanced services and
> perhaps wider annotation coverage. To help gather evidence of the
popularity of our services, to support our grant application,
> we are sending out a questionnaire to our users.
>
> Would it be possible to take 10 minutes to take part in our survey?:
http://www.AdvancedSurvey.com/default.asp?SurveyID=32355
>
> Also if you could pass on this mail to colleagues or to any
> appropriate news groups or mailing lists we'd be very grateful.
>
> Thanks ever so much for your time.
>
> Best wishes,
>
> Jennifer Clark
> GO Curator
>
>
>
>
>
>
> --
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
>
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683
>
>


Junjian Ni
Gramene Curator
G15, Bradfield Hall,
Cornell University,
Ithaca, NY 14853






From cer17 at cornell.edu  Thu Nov  3 16:19:41 2005
From: cer17 at cornell.edu (Claire E. Hebbard)
Date: Thu, 03 Nov 2005 16:19:41 -0500
Subject: Gramene Release V.19
Message-ID: <6.2.1.2.2.20051103152526.03a83e60@postoffice8.mail.cornell.edu>


Dear Cereal Researchers,

The Gramene database (<http://www.gramene.org>http://www.gramene.org) 
emails its registered users an announcement each time a new release is 
made. This announcement includes information on new or updated data and 
software.

Sincerely,
The Gramene Database

*****************************************************************
This work is funded by the National Science Foundation (NSF) and the 
USDA-Agricultural Research Service, and was previously funded by the USDA 
Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful 
to numerous collaborators and contributors for help in curation and for 
sharing their datasets and tools.

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

Gramene website features:


Navigation Bar changes:
"Genome Browser" link on the navigation bar replaced with "Genomes".
"CMap" link on the navigation bar replaced with "Maps".
"Protein" link on the navigation bar replaced with "Proteins".
"Ontology" link on the navigation bar replaced with "Ontologies".
"Gene" link on the navigation bar replaced with "Genes".

New and updated tutorials
All tutorials have been updated. Tutorials are available in HTML, PDF or 
PowerPoint versions to allow for different browser preferences. Many slides 
have notes pages to improve explanations.
Updated tutorials include Maps, Proteins, Ontologies, Genes, QTL and 
Literature.
Genomes and BLAST tutorials are two individual tutorials, whereas 
previously Genome Browser and Blast were a single tutorial.
New tutorials have been developed for Markers, GrameneMart (a tool in the 
Genomes database), website navigation and an overview of the modules.
Two new exercises have been created to help users conduct an ontology 
search and a comparison between species.

*********************
Genomes

Mapping to the Oryza sativa (japonica) genome of Rice SAGE tags obtained 
from MGOS (Magnaporthe Grisea Oryza Sativa Database).

Mapping to the Oryza sativa (japonica) genome of BAC ends of the following 
species, sequences provided by OMAP project.
Oryza coarctata
Oryza minuta

Mapping to the Oryza sativa (japonica) genome of Maize whole genome shot 
gun reads from JGI (Joint Genome Institute).

Mapping to the Oryza sativa (japonica) genome of Maize genes/loci sequences 
being assayed by the Panzea project, most sequences are maize unigenes.

Updated mapping of OMAP BAC ends for the following species.
Oryza alta
Oryza brachyantha

Updated mapping of PUTs (putative unique transcripts) downloaded from 
PlantGDB.
Oryza sativa
Hordeum vulgare
Sorghum bicolor
Triticum aestivum
Zea mays

Updated mapping of 3' Sorghum EST cluster from LGB(Laboratory of Genomics 
and Bioinformatics) at University of Georgia. 3' cluster sorghum Milestone 
version 3.0 replaced the 3' cluster sorghum Milestone version 2.0

Updated mapping of Ryegrass assembly by ViaLactia, the genomic sequences 
used by the assembly were cloned from a GeneThresher methyl-filtered library.

1307 of the previously unmapped Rice MPSS (Massively Parallel Signature 
Sequencing) oligo sequences were mapped to the Oryza sativa (japonica) genome.

33 of the previously unmapped Rice Oligos were mapped, these oligos are 
from NSF Rice Oligonucleotide Array Project

ContigView
The alignment feature query coordinates changed in this release
The alignment block coordinates no longer follow the BLAT output format, 
where the query coordinates are from the point of view of the reverse 
strand when the match is on the reverse strand. The query coordinates are 
always on the forward strand.
All the coordinates are 1-based.
Some track names changed, new names are more accurate, intuitive and 
consistent.
A new track named "Rice_FSTtransposon" replaced 2 old tracks "Rice_FST_Ds" 
and "Rice_FST_IS"
Oryza Sativa TE (transponsable element) track added at the bottom of the 
detail view.
*********************
BLAST

There is now a BLAST tutorial
*********************
Maps
    * In this build (v. 19) we present our initial release of the IRGSP 
build 4.0 rice genome assembly, to which we have mapped the RFLP markers 
from rice.
    * We have also added three maps of the recently-released set of Class I 
SSRs.
    * New BAC end sequence from wild Oryza spp. has been added to the map 
of the TIGR rice assembly; some other features have also been updated on 
that map.
    * Nine rice maps been updated with additional QTL and genes.
    * One new QTL map for maize was also added.

New Sequence and Physical Maps New QTL Map Updated Maps
Rice-Gramene IRGSP Assm 2005
Rice-Cornell Class I SSR (TIGR) 2005
Rice-Cornell Class I SSR (IRGSP) 2005
Rice-Cornell Class I SSR (93-11) 2005
Maize Bins QTL 2005

Features Added and Updated
Rice-GR TIGR Assm IRGSP Seq 2005

QTL Added
Rice-IRRI Lemont/Teqing RI RFLP QTL 2001
Rice-JRGP Nipponbare/Kasalath RFLP QTL 2000
Rice-JKU Asominori/IR24 RI RFLP QTL 1996

Genes Added
Rice-Cornell IR64/Azucena SSR 2001
Rice-Cornell BS125/2/BS125/WLO2 RFLP 2001
Rice-IGCN ZhaiYeQing 8/JingXi 17 1998
Rice-IRMI Integrated SSR 2003
Rice-JRGP Nipponbare/Kasalath RFLP 2000
Rice-Hokkaido Morphological 2000

*********************
Markers
The marker database now contains a total of 4,547,608 markers from more 
than 180 species.
The database has been updated with an additional 13,519 Class I SSRs from 
rice.
We have added
2,530,661 Genbank dbEST sequences from fifty species of Poaceae as  marker 
type "EST"
129,527 NCBI Unigene entries from six Poaceae species and 472,408 TIGR Gene 
Indexes from eight Poaceae species as marker type; "EST Cluster"; and
91,074 GenBank DNA sequences from Poaceae flagged as mRNA (excluding dbEST) 
entries from 162 species as marker type "mRNA"

The results table once again shows any number of results, even if more than 
1,000 markers result from a query. The search results are returned 
unsorted, however. Users may still sort the results by clicking on column 
headings, but sorting a large number (> 1,000) of markers will be slow.

Marker breakdown by species:
Species Markers
Barley (Hordeum spp.)                   535720
Maize (Zea spp.)                        1089433
Oat (Avena spp.)                        8215
Rice (Oryza spp.)                       1475049
Rye (Secale spp.)                       13260
Sorghum (Sorghum spp.)          260634
Sugarcane (Saccharum spp.)              339657
Wheat (Triticum spp. + Aegilops spp.)   787493
Other                                   38147

********************
Proteins

The Gramene protein database now provides curated information on SP-Trembl 
entries from family Poaceae (Grasses)

The protein database includes new and updated information on 68,123 gene 
products drawn from SwissProt (2074) and SP-TREMBL (66,049).

These proteins are annotated using Pfam, Prosite, TMHMM (for transmembrane 
domains), TargetP and Predotar (plastid, mitochrondrial and secretory 
pathway targeting) and Interpro categories. A total of 49,565 gene products 
are associated with 1,479 Gene Ontology terms.

You can search the protein database for entries by using either the 
SWISSPROT accession number / SPTrEMBL ID / Protein Sequence Identifier 
(Protein_ID) / GI number / protein name / gene name / species / cultivar.

The entries for Aegilops, Triticum, Avena and Hordeum link back to 
GrainGenes database.  Similarly the proteins from maize link back to the 
MaizeGDB.

********************
Ontologies
New: The ontology detail page now displays 'External references' and 
'Comments' associated with a given ontology term.

Gramene Taxonomy Ontology: NEW
Total number of terms = 2204. A total of 68,122 proteins, 1488 genes, 9871 
QTL and 163 mapset associations.

Gene Ontology: Updated
Total number of terms = 19,498. A total of 49,565 proteins and 21,369 
Ensembl genes are associated with 1,479 Gene Ontology terms.

Plant Ontology: Updated
Total number of terms = 684. Includes associations to rice genes only

Gramene Plant Growth Stage Ontology: No updates
Total number of terms = 236
The wheat, barley and oat growth stages have the same growth stage ontology.

Trait Ontology: Updated
Total number of terms = 693. A total of 428 genes and 9871 QTL are 
associated with the trait terms.

Environment Ontology:Updated:
Total number of terms = 490

The Ontology browser now displays the total number of objects 
(QTL/phenotype gene/EnsEMBL gene/proteins/mapsets) associated with the 
"term name". For example: genus "Oryza" has following associations:
64,137 data entries
55,238 proteins from various Oryza species
1488 genes
7302 QTL
109 map sets
********************
Genes and Alleles

Continually growing, Gramene release 19 presents a reorganized gene detail 
display page over the last release. Specifically, changes will be noted for 
allele, germplasm, nucleotide and protein sequences, and the associated 
features sections. Associated features included all trait (Trait Ontology), 
growth stage (Plant Ontology), plant anatomy parts (Plant Ontology), and 
gene ontology terms associated with a particular gene. Links to the Gramene 
Ontology have been provided as well.

For release 19, there were 151 genes curated and mapped on several rice 
genetic maps to display as interpolated phenotypes. These map positions 
were based on closely linked markers. All genes with gene symbols beginning 
with the letters "A" through "N" and for which information was available 
are included.

The Gramene Genes Database contains 1,488 genes from rice which have been 
characterized by phenotype. Among them, 425 genes have been fully annotated 
with phenotypic descriptions, associations to trait, plant and gene 
ontologies, map positions, alleles, phenotypic studies, germplasms, 
sequences, gene products, and related public references.

********************
QTL

There are 246 newly curated rice QTLs from recent publications that have 
been added to the database.
Collaborative and integrative efforts between Gramene and MaizeGDB 
continue, and 1,215 newly imported maize QTLs from MaizeGDB have been 
integrated into the Gramene QTL database.

Trait Ontology (TO) terms have been integrated with definitions of the 
associated traits of QTL.
This will also allow the users to browse QTL by searching traits in the 
Gramene Ontology Database.

The Gramene QTL database includes a total of 9,871 QTL
These QTL were identified for numerous agronomic traits in rice, maize, 
barley, oat, wheat, pearl millet, foxtail millet and wild rice.


************************************************************************
Subscribe to the Gramene-announce list to receive announcements of updates
to the Gramene site. To subscribe to a mailing list, send an e-mail to
majordomo at gramene.org. In the body of the e-mail write:
subscribe gramene
or
subscribe gramene-announce
************************************************************************
Claire Hebbard
Gramene Outreach Coordinator
G15 Bradfield Hall
Ithaca, NY 14853

Cereals are mankind's most important source of calories. Gramene can assist 
in research on agriculturally important features in rice, maize, wheat and 
other grasses. 
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From schmidt at cshl.edu  Fri Nov  4 13:52:54 2005
From: schmidt at cshl.edu (Steven Schmidt)
Date: Fri, 4 Nov 2005 13:52:54 -0500
Subject: Feedback Submission from the Gramene Live Site
In-Reply-To: <200511040233.jA42Xuci006952@filetta.cshl.org>
References: <200511040233.jA42Xuci006952@filetta.cshl.org>
Message-ID: <200511041352.54698.schmidt@cshl.edu>

Hi all,

The blast search is now up again for our new release.
The mart system and all other modules should be working also.
Sorry for the inconvenience.

-Steve

On Thursday 03 November 2005 09:33 pm, feedback_submission at www.gramene.org wrote:
>     *** Feedback from the Live Site ***
>
> refer_to_url: any concerned person
>
> comments: I send one query but didn't receive nay answer for it.
> Today I am trying to blast few sequences but it is not working
>
> Could you please help me soon in this regard
>

-- 
Steven Schmidt        www.gramene.org        516-367-6977
Cold Spring Harbor Laboratory
---
Committing to CVS is like voting -- do it early and often.





From j.bernier at cgiar.org  Thu Nov 10 03:49:32 2005
From: j.bernier at cgiar.org (Bernier, Jerome (IRRI))
Date: Thu, 10 Nov 2005 16:49:32 +0800
Subject: SSR marker position (Noel)
Message-ID: <C781839E63F2A140A7928F015DBBA650233F84@Hermes>

Hi, 

 

I am doing QTL mapping and am now analyzing my data. I find that in my population, RM 4915 seems to map at the beginning of chromosome 12 and RM2578 seems to map at the end of chromosome 7, which are not the expected chromosomes based on the TIGR pseudomolecule. Any possible explanations?

 

Thanks,

 

J?r?me Bernier

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From gregorysbrown at mac.com  Mon Nov 14 15:31:24 2005
From: gregorysbrown at mac.com (Gregory Brown)
Date: Mon, 14 Nov 2005 13:31:24 -0700
Subject: ftp download site down
Message-ID: <8B3519EB-1578-4905-B2A1-2576B35C1B76@mac.com>

Hello,

Congratulations on gramene release 19!  I am patiently waiting to  
download some of the new data.  However the ftp.gramene.org site has  
not been responding for a week now.  Do you have a tentative time for  
when the ftp site will be operational again?  Thanks.

Greg Brown



From Janet.Higgins at bbsrc.ac.uk  Wed Nov 16 04:31:51 2005
From: Janet.Higgins at bbsrc.ac.uk (Janet Higgins (JIC))
Date: Wed, 16 Nov 2005 09:31:51 -0000
Subject: CMap
Message-ID: <286D8A554155B54CBFB18EF26EE2F1690157B46E@jie2ksrv1.jic.bbsrc.ac.uk>

Previously I have put in a BAC ID eg AP003047 into Feature search and it
gives me a link to the rice TIGR Pseudomolecule Assembly . I can then
add the wEST 2003 map and view the correspondence between the rice BAC
and the wEST 2003 map.

I no longer get a hit on the rice TIGR Pseudomolecule Assembly when I
search with a BAC ID. The only map sets I get a link to are AGI FPC 2002
and I-Map(FPC). I am really interested in the predicted position of a
gene in wheat but I am not able to search with a TIGR Loci eg
Os01g08700.

What should I put in Feature Search to view the position of a gene or
BAC in the RICE pseudomolecules map so that I am then able to add the
wEST comparative map and view the correspondence between the 2 maps.

Thanks
Janet Higgins



From Janet.Higgins at bbsrc.ac.uk  Thu Nov 24 07:41:36 2005
From: Janet.Higgins at bbsrc.ac.uk (Janet Higgins (JIC))
Date: Thu, 24 Nov 2005 12:41:36 -0000
Subject: Aligning  rice pseudomolecules to wEST 2003
Message-ID: <286D8A554155B54CBFB18EF26EE2F1690157B474@jie2ksrv1.jic.bbsrc.ac.uk>

How do I align the wEST deletion map to the rice pseudomolecules map to
visualise the correspondences between these two map.  I can no longer
add the wEST 2003 as a comparative map?
Thanks
Janet



From matthews at greengenes.cit.cornell.edu  Mon Nov 28 12:42:09 2005
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Mon, 28 Nov 2005 12:42:09 -0500 (EST)
Subject: Aligning  rice pseudomolecules to wEST 2003
Message-ID: <200511281742.jASHg948021914@greengenes.cit.cornell.edu>

Hi Janet,
There's a pretty good set of wEST/rice comparative maps at TIGR,
http://www.tigr.org/tdb/e2k1/tae1/wr_figureview.shtml
regards,
- Dave

> Date: Thu, 24 Nov 2005 12:41:36 -0000
> From: "Janet Higgins \(JIC\)" <Janet.Higgins at bbsrc.ac.uk>
> To: <gramene at gramene.org>
> 
> How do I align the wEST deletion map to the rice pseudomolecules map to
> visualise the correspondences between these two map.  I can no longer
> add the wEST 2003 as a comparative map?
> Thanks
> Janet

-   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
David E. Matthews, Ph.D.          USDA-ARS Plant Genome Database Curator
Cornell University                Email: matthews at greengenes.cit.cornell.edu
Department of Plant Breeding                          Phone: +1-607-255-9951 
409 Bradfield Hall                                      Fax: +1-607-255-6683
Ithaca, New York 14853, USA             GrainGenes: http://wheat.pw.usda.gov



From luhong at iastate.edu  Mon Nov 28 11:43:33 2005
From: luhong at iastate.edu (Hong Lu)
Date: Mon, 28 Nov 2005 10:43:33 -0600 (CST)
Subject: Maps (Barley Vs Rice Genome)
Message-ID: <334310281010513310@webmail.iastate.edu>

Hello,

I am a graduate student at Iowa State University. I am interested in alignment
between plant genechips and rice genome. Last year I got alignment between
barley and rice genome from Gramene. But now, when I check it, I find it has
been updated. Would you like to send my the latest alignment file? Thanks. The
format I got last time is as below,

Hit_id	Feature_name	Chr_segment (may be ignored)	Strand	Feature_start
Feature_stop	Chromosome	Chr_Start	Chr_end
1	Barley1_00002	9632:30000001..34960948	1	0	72	4	32959322	32959394
1	Barley1_00002	9632:30000001..34960948	1	154	294	4	32959494	32959634
1	Barley1_00002	9632:30000001..34960948	1	322	459	4	32959766	32959903
2	Barley1_00006	9629:25000001..30000000	1	736	788	1	29809574	29809632

What's the version of rice genome that aligns those chips? The 3rd version from
Tigr?
ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_3.0/

In the directory ftp://ftp.gramene.org/pub/gramene/array_mapping/, I find 4
alignment files. Are those the alignment between chips and rice genome(ver 3)? 

Thanks you for your help and I am looking forward to hearing from you.

Hong




From weix at cshl.edu  Wed Nov 30 14:49:03 2005
From: weix at cshl.edu (Sharon Wei)
Date: Wed, 30 Nov 2005 14:49:03 -0500
Subject: Maps (Barley Vs Rice Genome)
In-Reply-To: <334310281010513310@webmail.iastate.edu>
References: <334310281010513310@webmail.iastate.edu>
Message-ID: <438E022F.8020802@cshl.edu>


Thanks for being interested in gramene mapping. Please find the updated 
mapping in the attachment.

The format of this file is as follows:
Hit_id   
Feature_Name       
Chr_segment(may be ignored)
Chr_strand
Feature_start
Feature_end 
Chromosome
Chr_start
Chr_end  
score(may be ignored)  
perc_id(may be ignored) 
CIGAR(may be ignore)

1       Barley1_00002   chr_4_6 1       1       72      4       
33022121        33022192        261     86      71M
1       Barley1_00002   chr_4_6 1       155     294     4       
33022293        33022432        261     86      139M
1       Barley1_00002   chr_4_6 1       323     459     4       
33022565        33022701        261     86      136M

Please be aware of the following coordinates changes:

# The alignment feature query coordinates changed in this release

    * The alignment block coordinates no longer follow the BLAT output
      format, where the query coordinates are from the point of view of
      the reverse strand when the match is on the reverse strand. The
      query coordinates are always on the forward strand.
    * All the coordinates are 1-based for both feature and chromosome.


You are right, the rice genome is the 3rd version from Tigr.
The files in ftp://ftp.gramene.org/pub/gramene/array_mapping/ are old 
alignment between chips and rice genome,
they are not the updated mapping.

Please feel free to ask if any more questions come up.


Sharon
Gramene Project


Hong Lu wrote:

>Hello,
>
>I am a graduate student at Iowa State University. I am interested in alignment
>between plant genechips and rice genome. Last year I got alignment between
>barley and rice genome from Gramene. But now, when I check it, I find it has
>been updated. Would you like to send my the latest alignment file? Thanks. The
>format I got last time is as below,
>
>Hit_id	Feature_name	Chr_segment (may be ignored)	Strand	Feature_start
>Feature_stop	Chromosome	Chr_Start	Chr_end
>1	Barley1_00002	9632:30000001..34960948	1	0	72	4	32959322	32959394
>1	Barley1_00002	9632:30000001..34960948	1	154	294	4	32959494	32959634
>1	Barley1_00002	9632:30000001..34960948	1	322	459	4	32959766	32959903
>2	Barley1_00006	9629:25000001..30000000	1	736	788	1	29809574	29809632
>
>What's the version of rice genome that aligns those chips? The 3rd version from
>Tigr?
>ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_3.0/
>
>In the directory ftp://ftp.gramene.org/pub/gramene/array_mapping/, I find 4
>alignment files. Are those the alignment between chips and rice genome(ver 3)? 
>
>Thanks you for your help and I am looking forward to hearing from you.
>
>Hong
>
>
>  
>

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From ware at cshl.edu  Wed Nov 30 18:15:48 2005
From: ware at cshl.edu (Ware, Doreen)
Date: Wed, 30 Nov 2005 18:15:48 -0500
Subject: Aligning  rice pseudomolecules to wEST 2003  (Noel)
Message-ID: <6F37486D54C31947A3B1414E62670432A11444@mailbox04.cshl.edu>

Hi All,

I would like to think that Dave could point them to our site for the
comparative map.   

Noel, we discussed the way the markers are placed now in bins it makes
it very difficult to get the genbank accession and a download of the
order.  I think it would be very useful to provide this list as a down
load associated with the map on CMap on the information page for the map
sets.  The same could be done for the maize and sorghum maps.   This
information would also be added to the new wheat page Claire has been
working on.

Doreen 



-----Original Message-----
From: owner-gramene at gramene.org [mailto:owner-gramene at gramene.org] On
Behalf Of Dave Matthews
Sent: Monday, November 28, 2005 12:42 PM
To: Janet.Higgins at bbsrc.ac.uk
Cc: Gramene mailgroup
Subject: Re: Aligning rice pseudomolecules to wEST 2003

Hi Janet,
There's a pretty good set of wEST/rice comparative maps at TIGR,
http://www.tigr.org/tdb/e2k1/tae1/wr_figureview.shtml
regards,
- Dave

> Date: Thu, 24 Nov 2005 12:41:36 -0000
> From: "Janet Higgins \(JIC\)" <Janet.Higgins at bbsrc.ac.uk>
> To: <gramene at gramene.org>
> 
> How do I align the wEST deletion map to the rice pseudomolecules map
to
> visualise the correspondences between these two map.  I can no longer
> add the wEST 2003 as a comparative map?
> Thanks
> Janet

-   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
-   -
David E. Matthews, Ph.D.          USDA-ARS Plant Genome Database Curator
Cornell University                Email:
matthews at greengenes.cit.cornell.edu
Department of Plant Breeding                          Phone:
+1-607-255-9951 
409 Bradfield Hall                                      Fax:
+1-607-255-6683
Ithaca, New York 14853, USA             GrainGenes:
http://wheat.pw.usda.gov




