Gramene Release 17.0

Molly Fogleman mam94 at cornell.edu
Thu Mar 31 13:12:49 EST 2005 

Dear Cereal Researchers,

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

Sincerely,
The Gramene Database


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

Gramene website features:
*********************
New Navigation Bar - Addition of Species Module to navigation bar. 
Removal of SSR Search from main navigation bar - can now be found under
the Marker (http://www.gramene.org/markers/index.html) database's
navigation bar.

New Species Module (http://www.gramene.org/species/index.html) -
Educational pages with information for the high school student up to the
researcher on each of the species contained in Gramene.

Resources (http://www.gramene.org/resources/index.html) - Addition of
"Tools for plant genome analysis" to Resources page.



Databases:
*********

QTL (updated)
************
The Gramene QTL database includes a total of 8,160 QTL identified for
numerous agronomic traits in rice, maize, barley, oat, wheat, pearl
millet, foxtail millet and wild rice.  150 newly curated QTL, including
some wheat QTL integrated from GrainGenes, have been added into the
database for this release.

Gramene now uses “Trait Ontology” terms (TO) to define the associated
traits of its QTL.  This also allows the users to browse the QTL by
searching for traits in the Gramene Ontology Database.



Genome Browser (updated)
**********************
- Import of the TIGR pseudomolecule assembly release 3 of IRGSP finished
sequence, and associated gene model predictions.

- Annotation of the TIGR gene models with protein domains, generated using
InterproScan. Annotations include;
      Interpro domains,
      Pfam domains,
      SMART domains,
      PROSITE profiles,
      PROSITE Patterns
      SUPERFAMILY families,
      ProDom domains,
      PIR SuperFamily families,
      TIGRFAM families,
      PRINTS motifs,
      Coil domans,
      Low complexity (seg) regions.

- GO terms associated with the above domains have been mapped to the TIGR
gene model transcripts.

- Addition of gene models predicted by the FGENESH Hidden Markov Model
(HMM)-based ab-initio gene prediction program

- Addition of gene models submitted directly to GenBank in the form of
nucleotide sequence annotations

- Mapping to the Oryza sativa (japonica) genome of BAC end sequences
generated by the OMAP project for the following species;
      Oryza alta,
      Oryza australiensis,
      Oryza glaberrima,
      Oryza punctata.

- Mapping to the Oryza sativa (japonica) genome of flanking sequence tags

    (FSTs);
    Rice T-DNA inserts,
    Rice Ds inserts.


New Genome Browser Features:

  - ContigView
      Addition of tracks to display the new OMAP and FST mappings.
Addition of an 'FST' configuration menu.

  - TransView/ProtView
      Addition of GO, Interpro and domain annotations to the display.

  - DomainView
      New page for the display of a given InterPro domain.

  - BlastView
      Addition of the new OMAP and FST data as searchable databases.

  - Migration from Ensembl v26 to Ensembl v28 code base and schema.


CMap (updated)
*************
In this release, we present the first two physical maps of wild relatives
of rice from the OMAP Project. There are also six new QTL maps, two
consensus maps from wheat, and the maize bin map. The maize IBM2 neighbors
map has been updated to the latest version released on MaizeGDB. The rice
TIGR assembly/IRGSP sequence map has been updated to correspond to release
3 of the TIGR Rice Pseudomolecules. The TIGR/IRGSP map also integrates the
tos17 mappings that were previously shown on Rice-Gramene Tos17 Insert Map
2004; the latter map has thus been removed.

New Consensus and Physical Maps:
Wheat-Composite 2004
Wheat-Consensus SSR 2004
Maize-Bins
O. nivara-OMAP FPC 2005
O. rufipogon-OMAP FPC 2005

New QTL Maps:
Rice-Cornell V20A/glab QTL 2004
Rice-JUT IR36/Genj QTL 2004
Barley-UMN Fred/Stan QTL 2003
Wheat-UMN Sumai/Stoa QTL 1999
Wheat-UMN Sumai/Stoa QTL 2003
Wheat-UMN ND2603/Butte QTL 2003


Updated Maps:
Maize-IBM2 Neighbors 2004
(replaces Maize-IBM2 Neighbors June 2003)
Rice-GR TIGR Assm IRGSP Seq 2005
(replaces Rice-GR TIGR Assm IRGSP Seq 2004)
Removed Rice-Gramene Tos17 Insert Map 2004.
The tos17 mappings have been integrated into Rice-GR TIGR Assm IRGSP Dec
2004.



Markers (updated)
*****************
The marker database now contains a total of 297,656 markers from of 11
species. The new search interface allows users to filter their marker
searches based on marker types and the species of origin. The main search
page features a link to download in tab-delimited format the results of
any search.




Protein (updated)
**************
The protein database now provides information on SP-Trembl enteries from
rice and other species such as Aegilops, Avena, Hordeum, Lolium,
Pennisetum, Saccharum, Secale, Sorghum, Triticum, and Zea.

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 the
GrainGenes database. e.g. Protochlorophyllide reductase from Oat.
http://www.gramene.org/db/protein/protein_search?protein_id=143157



Ontology (updated)
****************
The Ontology browser now displays the total number of objects
(QTL/phenotype gene/EnsEMBL gene/proteins) associated with the "term name".

For example "alpha-amylase activity (GO:0004556) "
http://www.gramene.org/db/ontology/search_term?id=GO:0004556

This term has :
Total Number of Annotations: 105 objects, 105 associations protein: 89
proteins (wheat(18), sorghum(2), rice(28), maize(10), barley(26), wild
oats(2), tausch's goatgrass(3))
Ensembl gene:         16 rice Ensembl genes

For help, please see the updated help document at
http://www.gramene.org/documentation/ontology_help.html



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Molly Fogleman
Gramene Outreach Coordinator
409 Bradfield Hall
Cornell University
Ithaca, NY 14853
Phone:(607) 255-9951
Fax: (607) 255-6683

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