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<FONT FACE="Times CE"><SPAN STYLE='font-size:12.0px'>Please remove me from your mailing list!<BR>
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Thanks<BR>
<BR>
<BR>
On 3/17/06 8:52 AM, "Claire Hebbard" <cer17@cornell.edu> wrote:<BR>
<BR>
</span></font><BLOCKQUOTE><FONT FACE="Times CE"><SPAN STYLE='font-size:12.0px'>Dear Cereal Researchers, <BR>
<BR>
The Gramene database (www.gramene.org <a href="http://www.gramene.org"><http://www.gramene.org></a> ) <BR>
emails its registered users an announcement each time a new release is <BR>
made. This announcement includes information on new or updated data and <BR>
software at Gramene. <BR>
<BR>
For the current release notes (shown below), visit www.gramene.org/documentation/release_notes/releasenotes20.html <a href="http://www.gramene.org/documentation/release_notes/releasenotes20.html"><http://www.gramene.org/documentation/release_notes/releasenotes20.html></a> . <BR>
Data and statistics are located at <a href="ftp://ftp.gramene.org/pub/gramene/release20/data/">ftp://ftp.gramene.org/pub/gramene/release20/data/</a> <BR>
<BR>
The next release is anticipated in May. <BR>
<BR>
Sincerely, <BR>
The Gramene Database <BR>
***************************************************************** <BR>
This work is funded by the National Science Foundation (NSF) and the <BR>
USDA-Agricultural Research Service, and was previously funded by the USDA <BR>
Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful <BR>
to numerous collaborators and contributors for help in curation and for <BR>
sharing their datasets and tools. <BR>
***************************************************************** <BR>
****************************************************************** <BR>
<BR>
<BR>
<BR>
This release includes: <BR>
<BR>
****************************************************************** <BR>
Website features: <BR>
<BR>
The new layout of the website has been successful with users. Remember that the Gramene logo is your <BR>
link to the Gramene Home Page, and the species pages can be accessed through the images on the footer. <BR>
New users may find it useful to use the Site Map (listed under "help") to review the website layout. <BR>
<BR>
FAQ's have changed format, and can now be searched through a link at the <B>bottom left</b> of the FAQ page. <BR>
To submit a question to the FAQ, send a question via the "feedback" link at the top of every page, <BR>
or use the mailing list (www.gramene.org/mailarch/ <a href="http://www.gramene.org/mailarch/"><http://www.gramene.org/mailarch/></a> <a href="http://dev.gramene.org/mailarch/"><http://dev.gramene.org/mailarch/>;</a>). The FAQ page <BR>
will be simplified eventually, but for now users should simply select the module they have a question for, <BR>
or use the search option at the bottom left of the page. <BR>
<BR>
New species page for wheat (www.gramene.org/triticum/triticum_intro.html <a href="http://www.gramene.org/triticum/triticum_intro.html"><http://www.gramene.org/triticum/triticum_intro.html></a> ) There has also been <BR>
some restructuring of the species pages, with a new species homepage <BR>
(www.gramene.org/species/index.html <a href="http://www.gramene.org/species/index.html"><http://www.gramene.org/species/index.html></a> ), with <a href="http://dev.gramene.org/species/index.html"><http://dev.gramene.org/species/index.html></a> links to a general cereal introduction and statistics. <BR>
<BR>
****************************************************************** <BR>
<BR>
Genomes Release Notes <BR>
New Genomes Data <BR>
<BR>
* Mapping to the Oryza sativa (japonica) genome of 14,589 rice SSR tags obtained from gramene markers database. <BR>
* Mapping to the Oryza sativa (japonica) genome of 5,416 rice QTLs anchored by boundary markers <BR>
* Updated 504 full-length Zea mays clones deposited with GenBank as of 26-Jan-2006 in Maize Accessioned BAC Browser <BR>
* Mapping to the full-length Zea mays clones of the 61 sets of sequences that are mapped to <BR>
rice TIGR v3 assembly. These 61 datasets include many datasets that are already mapped to Maize clones <BR>
and many new datasets that are mapped to Maize clones for the 1st time. For a complete list, go to the in silicon <BR>
mapping summary (www.gramene.org/documentation/Alignment_docs/to_Maize/summary.html <a href="http://www.gramene.org/documentation/Alignment_docs/to_Maize/summary.html"><http://www.gramene.org/documentation/Alignment_docs/to_Maize/summary.html></a> ). <BR>
<BR>
Some of these new sequence sets are <BR>
*Maize_BACends: 10,4007 out of 472,700 sequences were mapped <BR>
*Maize_wgs_JGI: 222,255 out of 1,124,441 sequences were mapped <BR>
*Maize_ArrayGenes_NSF58K: 2,910 out of 57,452 sequences were mapped. <BR>
<BR>
New Genomes Features <BR>
<BR>
*Zea mays accessioned clones ContigView. <BR>
**The alignment feature coordinates representation changed in this release, <BR>
and is consistant with the coordinates representation in rice genome browser <BR>
**The alignment block coordinates no longer follow the BLAT output format, where the query coordinates are <BR>
from the point of view of the reverse strand when the match is on the reverse strand. The query coordinates <BR>
are always on the forward strand. <BR>
**All the coordinates are 1-based. <BR>
*Track names changed to be consistant with Oryza sativa genome browser <BR>
<BR>
****************************************************************** <BR>
BLAST Release Notes <BR>
<BR>
The following databases have been added; <BR>
<BR>
* Maize - cDNAs (FGENESH gene models) <BR>
* Maize - Peptides (FGENESH gene models) <BR>
* Maize - Clones (GenBank) <BR>
<BR>
The following databases have been updated; <BR>
<BR>
* All species - UniProtKB (SPTr) Peptides <BR>
<BR>
****************************************************************** <BR>
Maps Release Notes <BR>
<BR>
In this build, we present one new genetic map each from barley and rice, and a new rice QTL map. <BR>
Additional QTL have also been added to four existing rice QTL maps. Nearly 3,000 maize genes have <BR>
been positioned on the maize bin map. The map of the rice TIGR assembly has been updated to reflect <BR>
all the latest features mapped to the rice genome, which should synchronize the CMap and Ensembl <BR>
versions of the map. <BR>
<BR>
New Genetic Maps<BR>
* Barley-Barley consensus 2003 <BR>
* Rice-CIAT SSR 2006 <BR>
New QTL Map <BR>
* Rice-CNHAU Zhenshan97/ H94 DH SSR QTL 2005 <BR>
<BR>
Updated Maps <BR>
* QTL Added <BR>
o Rice-TKU Asominori/IR24 RI RFLP QTL 1996 <BR>
o Rice-TTU IR58821/IR52561 RI AFLP QTL 2002 <BR>
o Rice-NDSU EM93-1//EM93-1/SS18-2 BC1 SSR QTL 2004 <BR>
o Rice-CNHZAU Zhenshan97/Minghui63 RI QTL 2002 <BR>
* Features Added and Updated <BR>
o Rice-GR TIGR Assm IRGSP Seq 2005 <BR>
o Maize Bins <BR>
****************************************************************** <BR>
<BR>
Markers Release Notes <BR>
<BR>
The markers database has been updated with an additional 1,745,793 markers, most notably 1,099,874 <BR>
genomic survey sequences from maize and related species. It now contains a total of 6,293,401 markers <BR>
from more than 180 species. <BR>
<BR>
Marker breakdown by species: <BR>
Barley (Hordeum spp.)--535,720 <BR>
Maize (Zea spp.)--2,622,201 <BR>
Oat (Avena spp.)--8,215 <BR>
Rice (Oryza spp.)--1,651,823 <BR>
Rye (Secale spp.)--13,262 <BR>
Sorghum (Sorghum spp.)-- 312,845 <BR>
Sugarcane (Saccharum spp.)--339,657 <BR>
Wheat (Triticum spp. + Aegilops spp.) 798,051 <BR>
Other 38,154 <BR>
<BR>
****************************************************************** <BR>
Proteins Release Notes <BR>
<BR>
The Gramene protein database provides curated information on SP-Trembl entries from family <BR>
Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), <BR>
TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. <BR>
Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment <BR>
Ontology (EO) are used to provide functional characteristics. <BR>
<BR>
In this release we have: <BR>
<BR>
* Total number of proteins: 76,512 <BR>
* Proteins from SWISS-PROT: 2,304 <BR>
* Proteins from TrEMBL: 74,208 <BR>
<BR>
****************************************************************** <BR>
Ontologies Release Notes <BR>
<BR>
* Ontologies: Various ontologies and their associations were updated. For more details on <BR>
different types of ontologies please visit the ontology home page. <BR>
<BR>
The ontologies provided are: <BR>
**Gene Ontology: <BR>
**Plant Ontology: <BR>
**Gramene Plant Growth Stage Ontology: <BR>
** Trait Ontology: <BR>
**Gramene Taxonomy Ontology: <BR>
**Environment Ontology: The Environment Ontology now provides associations to genes, <BR>
proteins and EST libraries from rice <BR>
<BR>
****************************************************************** <BR>
Genes and Alleles Release Notes <BR>
<BR>
Continually growing, Gramene release 20 presents a reorganized gene search interface over the <BR>
last release. In addition to the generic search, the users can use keyword to search the Genes database. <BR>
The search can be restricted to any one field, such as gene symbol, gene name, chromosome number, <BR>
ontology terms (trait ontology, plant structure, growth stage, gene ontology, environment ontology), <BR>
GenBank accession and Gramene protein accession. If necessary, the users also can do a search in <BR>
all these fields. <BR>
<BR>
As a collaboration and integration effort between Gramene and MaizeGDB, 6,676 newly imported <BR>
maize genes from MaizeGDB have been integrated into the Gramene Genes database. Together with <BR>
1,525 rice genetically identified genes, the total number of genes in the Genes database has reached 8,201. <BR>
<BR>
A more detailed genes database statistics report can be found at <BR>
<a href="ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/gene_statistics">ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/gene_statistics</a> . <BR>
****************************************************************** <BR>
QTL Release Notes <BR>
<BR>
The Gramene QTL database includes a total of 10,147 QTL identified for numerous agronomic <BR>
traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice. <BR>
<BR>
A significant improvement in this release is the integration of rice QTL to the rice genome. Following <BR>
the protocol developed in our database, 5,416 rice QTL with directly associated markers on the <BR>
genome have been anchored to the rice genome. This will allow users to access a specific genome <BR>
region corresponding to a QTL or to browse QTL by searching for traits on the rice genome browser. <BR>
<BR>
In addition, 276 newly curated rice QTLs from the recent publications have been add to the database. <BR>
A more detailed QTL database statistics report can be found at <BR>
<a href="ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/qtl_statistics">ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/qtl_statistics</a> . <BR>
<BR>
<BR>
<BR>
****************************************************************** <BR>
******************************************************************<BR>
<BR>
Claire Hebbard<BR>
Gramene Outreach Coordinator<BR>
<BR>
G15 Bradfield Hall<BR>
Cornell University<BR>
Ithaca, NY 14853<BR>
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</span></font></blockquote><FONT FACE="Times CE"><SPAN STYLE='font-size:12.0px'><BR>
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</span></font><SPAN STYLE='font-size:12.0px'><FONT FACE="Courier, Courier New"><BR>
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************************************<BR>
George Heine<BR>
Department of Plant Cellular<BR>
and Molecular Biology<BR>
218 Rightmire Hall<BR>
1060 Carmack Rd<BR>
Columbus OH 43210<BR>
(614) 688-4954<BR>
Heine.22@osu.edu<BR>
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