Gramene Release 16.0

[Molly Fogleman]

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


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Gramene website features:
*********************
Gramene Tips – Helpful tips on using the Gramene Database are now located
on the home page.  A new tip will appear each time the homepage is opened.


Databases:
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QTL (updated)
************
The Gramene QTL database includes a total of 8,015 QTL identified for
numerous agronomic traits in rice, maize, barley, oat, pearl millet,
foxtail millet and wild rice.  In this release, approximately 300 newly
curated rice QTL from recent publications were added into the database.


Genome Browser (updated)
**********************
The Genome Browser software has been updated to provide a range of
performance and functionality enhancements.  Specifically, the code and
database are now based on Ensembl's v26 (November 2004)
release(http://www.ensembl.org).

A new naming convention for browser tracks has been implemented as
follows; <Species>_<Type>_<Project>. For example:

1. Rice_GeneModel_TIGR (was tigr_gene trans.) represents gene models for
rice, produced by The Institute for Genome Research (TIGR).

2. RiceNivara_BACend_OMAP (was Rice_Nivara_BACend) represents BAC end
sequences for the nivara rice species, sequenced in support of the Oryza
Map Alignment Project (OMAP).

Browser tracks can now be toggled on/off using the menus at the top of the
display panel. This has replaced the 'Advanced...' option under the
'Display' menu. Browser tracks have been categorized into four classes,
each with its own menu:

1. GSS - tracks derived from Genome Survey Sequences (GSS), e.g.
Maize_HiCot_Bennetzen, Maize_HiCotCluster_TIGR

2. EST - tracks derived from Expressed Sequence Tag (EST) sequences, e.g.
Wheat_EST, Wheat_ESTCluster_TUG

3. Markers - tracks derived from marker sequences, e.g. Rice_Marker,
Maize_Marker

4. Features - tracks derived from sequences apart from the above, e.g.
Rice_GeneModel_TIGR, Rice_BAC


New tracks for this release are Ryegrass_EST_Vialactia and
Ryegrass_ESTCluster_Vialactia. Data for the following tracks have been
updated: ESTCluster_TGI for all species, and Rice_Brachyantha_BACend.

Additional links to CMap have been added; MapView now links to the
corresponding chromosome for the Rice TIGR Assembly map, and the 'Jump to'
menu of the ContigView browser links to the corresponding region.

A new view, FeatureView, displays the location of all alignments of the
selected feature against the genome. The page is linked from features
displayed in the ContigView browser tracks. FeatureView is a convenient
entry point for linking of external identifiers to the Gramene Browser.

Other additional views, KaryoView and ChromoView, allow users to display
their own data on the rice karyotype and chromosome images respectively.
These pages are linked from MapView.



BLAST (updated)
**************
Links from the BlastView display to ContigView have been improved. 
Alignments are now displayed graphically as a new ContigView track.



CMap (updated)
*************
In this release, we present five new QTL maps from rice and six updated
genetic and physical maps for rice, maize, and sorghum:

QTL Maps:
Rice-CNZU IR1552/Azu RI QTL 2004
Rice-NDSU EM93/SS18 BC QTL 2004
Rice-JUT Patnai/Goai F2 QTL 2004
Rice-Cornell Jef/Oruf BC QTL 2004
Rice-TNCGEB CT9993/IR6226 QTL 2004

Updated Maps:
Rice-GR TIGR Assm IRGSP Seq 2004
(replaces Rice-Gramene TIGR Assembly 2004)
Rice-Gramene Tos17 Insert Map 2004
(updated name for Rice-Gramene Tos17 Insertion Map 04)
Maize-AGI FPC Map Oct 2004
(replaces Maize-AGI FPC MAP June 2004)
Maize-Gramene Curated AGI FPC Oct 2004
(replaces Gramene Curated AGI FPC June 2004)
Sorghum-Klein 2004
(replaces Sorghum-Klein 2000)
Sorghum-TAMU FPC 2004
(replaces Sorghum-TAMU FPC 2000)

In past releases, Gramene chose to create correspondences from QTL maps
only to non-QTL maps of the same species, but in this release, Gramene has
chosen to expand the correspondences to all other species, greatly
increasing the number of correspondences to our QTL maps.

Additionally, Gramene is using the newest version of CMap, the forthcoming
0.13. Some changes include:

Expanded/reorganized/hidden menus: Many more options for controlling the
maps are now available. As such, most of the menus remain hidden until the
user requests to see them.

New map glyphs/data: Above each map is a number in square brackets
indicating the number of features on the map. Running vertically are pairs
of arrows pointing up and down which allow you to crop a map. Below the
maps are "-" and "+" magnification buttons.

Comparative map selection: The selection form for comparative maps is
significantly larger now and is hidden beneath the "Comparison" button.
Clicking a map set name causes all the available maps of that map set to
display in the map selection form. It's also possible to choose more than
one comparative map.

Filtering of features: It's easier to choose which features to see based
on their type and whether they have correspondences. Under the "Options"
menu is a table allowing the user to choose for each feature type whether
to ignore it completely, display only if there is a correspondence, or to
always display features of that type.

Aggregating of correspondences: The user can decrease the number of lines
indicating correspondences by aggregating them to 1 or lines that are
color-coded to indicate the number of correspondences.

Magnification: It's significantly easier to increase and decrease the
drawn size of the maps.


Protein (updated)
**************
The total number of rice protein entries now available in Gramene is
48,467. Of these, about 75% of them have annotation to Gene Ontology
terms.


Mutant (updated)
**************
The Gramene Mutant genes database contains 1,408 genes from rice
characterized by phenotype. Among them, 424 genes have been fully
annotated with phenotypic descriptions, associations to trait, plant and
gene ontologies, map positions, alleles, phenotypic studies, germplasms,
sequences and gene products, and related public references. Other genes in
the database are currently under curation. In this release, 88 new rice
phenotype-related genes from recent publications were added.


Ontology (updated)
****************

The Gene (GO), Plant (PO and GRO), Trait (TO) and Environment (EO)
ontologies have been updated with their most recent version. This includes
the updates and addition of new associations to rice proteins and mutants.


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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