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George Heine
Heine.22 at osu.edu
Fri Mar 17 09:21:40 EST 2006
Please remove me from your mailing list!
Thanks
On 3/17/06 8:52 AM, "Claire Hebbard" <cer17 at cornell.edu> wrote:
> Dear Cereal Researchers,
>
> The Gramene database (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 at Gramene.
>
> For the current release notes (shown below), visit
> www.gramene.org/documentation/release_notes/releasenotes20.html
> <http://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
> *****************************************************************
> 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.
> *****************************************************************
> ******************************************************************
>
>
>
> This release includes:
>
> ******************************************************************
> 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://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
> <http://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
> <http://www.gramene.org/species/index.html> ), with
> <http://dev.gramene.org/species/index.html> links to a general cereal
> introduction and statistics.
>
> ******************************************************************
>
> 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
> <http://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
>
> ******************************************************************
> 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
>
> ******************************************************************
> 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
> ******************************************************************
>
> 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
>
> ******************************************************************
> 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
>
> ******************************************************************
> 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
>
> ******************************************************************
> 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 .
> ******************************************************************
> 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 .
>
>
>
> ******************************************************************
> ******************************************************************
>
> Claire Hebbard
> Gramene Outreach Coordinator
>
> G15 Bradfield Hall
> Cornell University
> Ithaca, NY 14853
>
>
>
>
>
>
>
>
>
>
>
>
> `
************************************
George Heine
Department of Plant Cellular
and Molecular Biology
218 Rightmire Hall
1060 Carmack Rd
Columbus OH 43210
(614) 688-4954
Heine.22 at osu.edu
************************************
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