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Dear Cereal Researchers,
<br>
<br>
The Gramene database (<a class="moz-txt-link-abbreviated"
href="http://www.gramene.org">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 <a
class="moz-txt-link-abbreviated"
href="http://www.gramene.org/documentation/release_notes/releasenotes20.html">www.gramene.org/documentation/release_notes/releasenotes20.html</a>.
<br>
Data and statistics are located at <a class="moz-txt-link-freetext"
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 (<a class="moz-txt-link-abbreviated"
href="http://www.gramene.org/mailarch/">www.gramene.org/mailarch/</a> <a
class="moz-txt-link-rfc2396E" 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 (<a class="moz-txt-link-abbreviated"
href="http://www.gramene.org/triticum/triticum_intro.html">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>
(<a class="moz-txt-link-abbreviated"
href="http://www.gramene.org/species/index.html">www.gramene.org/species/index.html</a>),
with<a class="moz-txt-link-rfc2396E"
href="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 (<a class="moz-txt-link-abbreviated"
href="http://www.gramene.org/documentation/Alignment_docs/to_Maize/summary.html">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 class="moz-txt-link-freetext"
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 class="moz-txt-link-freetext"
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>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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