Gramene V20 release

Fri Mar 17 08:52:14 EST 2006

Dear Cereal Researchers,

The Gramene database (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 at Gramene.

For the current release notes (shown below), visit 
www.gramene.org/documentation/release_notes/releasenotes20.html.
Data and statistics are located at 
ftp://ftp.gramene.org/pub/gramene/release20/data/

The next release is anticipated in May.

Sincerely,
The Gramene Database
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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.
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This release includes:

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Website features:

The new layout of the website has been successful with users. Remember 
that the Gramene logo is your
link to the Gramene Home Page, and the species pages can be accessed 
through the images on the footer.
New users may find it useful to use the Site Map (listed under "help") 
to review the website layout.

FAQ's have changed format, and can now be searched through a link at the 
*bottom left* of the FAQ page.
To submit a question to the FAQ, send a question via the "feedback" link 
at the top of every page,
or use the mailing list (www.gramene.org/mailarch/ 
<http://dev.gramene.org/mailarch/>). The FAQ page
will be simplified eventually, but for now users should simply select 
the module they have a question for,
or use the search option at the bottom left of the page.

New species page for wheat 
(www.gramene.org/triticum/triticum_intro.html) There has also been
some restructuring of the species pages, with a new species homepage
(www.gramene.org/species/index.html), with links to a general cereal 
introduction and statistics.

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Genomes Release Notes
 New Genomes Data

       * Mapping to the Oryza sativa (japonica) genome of 14,589 rice 
SSR tags obtained from gramene markers database.
       * Mapping to the Oryza sativa (japonica) genome of 5,416 rice 
QTLs anchored by boundary markers
       * Updated 504 full-length Zea mays clones deposited with GenBank 
as of 26-Jan-2006 in Maize Accessioned BAC Browser
       * Mapping to the full-length Zea mays clones of the 61 sets of 
sequences that are mapped to
rice TIGR v3 assembly. These 61 datasets include many datasets that are 
already mapped to Maize clones
and many new datasets that are mapped to Maize clones for the 1st time. 
For a complete list, go to the in silicon
mapping summary 
(www.gramene.org/documentation/Alignment_docs/to_Maize/summary.html).

Some of these new sequence sets are
       *Maize_BACends: 10,4007 out of 472,700 sequences were mapped
       *Maize_wgs_JGI: 222,255 out of 1,124,441 sequences were mapped
        *Maize_ArrayGenes_NSF58K: 2,910 out of 57,452 sequences were 
mapped.

   New Genomes Features

*Zea mays accessioned clones ContigView.           
           **The alignment feature coordinates representation changed in 
this release,
and is consistant with the coordinates representation in rice genome 
browser
           **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.
*Track names changed to be consistant with Oryza sativa genome browser

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   BLAST Release Notes

   The following databases have been added;

       * Maize - cDNAs (FGENESH gene models)
       * Maize - Peptides (FGENESH gene models)
       * Maize - Clones (GenBank)

   The following databases have been updated;

       * All species - UniProtKB (SPTr) Peptides

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   Maps Release Notes

   In this build, we present one new genetic map each from barley and 
rice, and a new rice QTL map.
Additional QTL have also been added to four existing rice QTL maps. 
Nearly 3,000 maize genes have
been positioned on the maize bin map. The map of the rice TIGR assembly 
has been updated to reflect
all the latest features mapped to the rice genome, which should 
synchronize the CMap and Ensembl
versions of the map.

New Genetic Maps
       * Barley-Barley consensus 2003
       * Rice-CIAT SSR 2006
New QTL Map
       * Rice-CNHAU Zhenshan97/ H94 DH SSR QTL 2005

Updated Maps
       * QTL Added
             o Rice-TKU Asominori/IR24 RI RFLP QTL 1996
             o Rice-TTU IR58821/IR52561 RI AFLP QTL 2002
             o Rice-NDSU EM93-1//EM93-1/SS18-2 BC1 SSR QTL 2004
             o Rice-CNHZAU Zhenshan97/Minghui63 RI QTL 2002
       * Features Added and Updated
             o Rice-GR TIGR Assm IRGSP Seq 2005
             o Maize Bins
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   Markers Release Notes

The markers database has been updated with an additional 1,745,793 
markers, most notably 1,099,874
genomic survey sequences from maize and related species. It now contains 
a total of 6,293,401 markers
from more than 180 species.

Marker breakdown by species:
   Barley (Hordeum spp.)--535,720
   Maize (Zea spp.)--2,622,201
   Oat (Avena spp.)--8,215
   Rice (Oryza spp.)--1,651,823
   Rye (Secale spp.)--13,262
   Sorghum (Sorghum spp.)-- 312,845
   Sugarcane (Saccharum spp.)--339,657
   Wheat (Triticum spp. + Aegilops spp.)    798,051
   Other     38,154

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Proteins Release Notes

   The Gramene protein database provides curated information on 
SP-Trembl entries from family
Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for 
transmembrane domains),
TargetP and Predotar (plastid, mitochrondrial and secretory pathway 
targeting) and Interpro assignments.
Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) 
and Environment
Ontology (EO) are used to provide functional characteristics.

   In this release we have:

       * Total number of proteins: 76,512
       * Proteins from SWISS-PROT: 2,304
       * Proteins from TrEMBL: 74,208

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   Ontologies Release Notes

       * Ontologies: Various ontologies and their associations were 
updated. For more details on
different types of ontologies please visit the ontology home page.

The ontologies provided are:
        **Gene Ontology:
        **Plant Ontology:
        **Gramene Plant Growth Stage Ontology:
        ** Trait Ontology:
        **Gramene Taxonomy Ontology:
        **Environment Ontology: The Environment Ontology now provides 
associations to genes,
proteins and EST libraries from rice

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   Genes and Alleles Release Notes

   Continually growing, Gramene release 20 presents a reorganized gene 
search interface over the
last release. In addition to the generic search, the users can use 
keyword to search the Genes database.
The search can be restricted to any one field, such as gene symbol, gene 
name, chromosome number,
ontology terms (trait ontology, plant structure, growth stage, gene 
ontology, environment ontology),
GenBank accession and Gramene protein accession. If necessary, the users 
also can do a search in
all these fields.

   As a collaboration and integration effort between Gramene and 
MaizeGDB, 6,676 newly imported
maize genes from MaizeGDB have been integrated into the Gramene Genes 
database. Together with
1,525 rice genetically identified genes, the total number of genes in 
the Genes database has reached 8,201.

   A more detailed genes database statistics report can be found at
ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/gene_statistics 
.
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QTL Release Notes

   The Gramene QTL database includes a total of 10,147 QTL identified 
for numerous agronomic
traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet 
and wild rice.

   A significant improvement in this release is the integration of rice 
QTL to the rice genome. Following
the protocol developed in our database, 5,416 rice QTL with directly 
associated markers on the
genome have been anchored to the rice genome. This will allow users to 
access a specific genome
region corresponding to a QTL or to browse QTL by searching for traits 
on the rice genome browser.

   In addition, 276 newly curated rice QTLs from the recent publications 
have been add to the database.
A more detailed QTL database statistics report can be found at
ftp://ftp.gramene.org/pub/gramene/release20/data/statistics/qtl_statistics 
.

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Claire Hebbard
Gramene Outreach Coordinator

G15 Bradfield Hall
Cornell University
Ithaca, NY 14853

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