Gramene Release 18.0

Chengzhi Liang liang at cshl.edu
Tue Jul 19 11:51:14 EDT 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

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Gramene is funded by a Plant Genome Initiative grant from the National 
Science Foundation and a Specific Cooperative Agreement through the USDA 
Agricultural Research Service, and was previously supported by an IFAFS grant 
from the USDA Cooperative State Research and Education Service (CSREES).
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*******************
Release 18: 07/2005
*******************

Gramene website changes:
***********************

There are two major changes to the website: one is using Gene to replace 
previous Mutant in navigation bar, another one is the addition 
GrameneMart link in Genome Browser home page.

New Genome Browser Data:
***********************

- Mapping to the Oryza sativa (japonica) genome of flanking
  sequences for the Oryza sativa SNPs from NCBI's dbSNP build 34. 
   - Alignments were performed using the Ensembl Variation mapping
     pipeline which in turn uses the SSAHA algorithm.
   - Of the ~3,900,000 rice SNPs in dbSNP, ~2,900,000 were mapped to the
     genome; 2,700,000 to a unique location.

 - Mapping to the Oryza sativa (japonica) genome of Affymetrix
   concensus sequences for array data for the following species;
   - wheat (including Triticum aestivum, T. monococcum, T. turgidum, and 
     Aegilops tauschii), 61115 sequences, of which 21616 (35.35%) mapped.
   - rice (Oryza sativa), 57194 sequences, of which 47729 (83.45%) mapped.
   - maize (Zea mays), 17555 sequences, of which 10132 (57.72%) mapped.

- Mapping to the Oryza sativa (japonica) genome of partial genome
  assemblies (GSS clusters) for Zea mays (maize). Data supplied by
  Iowa State University. 214471 sequences, of which 45146 (21.05%)
  mapped.

- Mapping to the Oryza sativa (japonica) genome of rice oligo array
  sequences. Data supplied by TIGR. 20230 sequences of which 18884
  (93.3%) mapped. Alignments in the UTR regions of the TIGR gene
  models are classed as unmapped (will be added later).

- Mapping to the Oryza sativa (japonica) genome of rice MPSS
  (Massively Parallel Signature Sequencing) sequences. Data supplied
  by Blake Meyers at University of Delaware. 93301 sequences, of
  which 92735 (99.4%) mapped. Alignments that cross an exon boundary,
  or map to organelles, are classed as unmapped (will be added later).

- Updated mapping of NCBI dbEST sequences for Sugarcane to the Oryza sativa 
  (japonica) genome. 255984 sequences, of which 151942 (59.36%) mapped.


New Genome Browser Features:
***************************

- Introduction of GrameneMart
  - Easy and interactive access to bulk data downloads.
  - Retrieval of sequences and genome annotations using a variety of
    filters to constrain retrieved results.
  - Filters include such things as genomic location and the presence
    or absence of specific annotations.
  - Data can be returned in a variety of formats, inluding HTML,
    text, FASTA, and even Microsoft Excel.
  - GrameneMart is the Gramene implementation of BioMart.

- SnpView;
  - New page for the display of a given SNP. 

- TransView, ProtView;
  - Addition of information for SNPs that map in the location of the
    gene,
  - Options to add SNP markup to the cDNA/peptide sequences,
  - Table of SNPs and their consequence to the protein,

- GeneSnpView
  - New page for the graphical representation of SNP info in the
    context of a gene. 

- ContigView
  - Addition of new tracks to display the SNP, Affymetrix concensus,
    partial genome assembly, oligo array and MPSS mappings.


Ontology Database:
*****************

 - New: The Gramene's taxonomy ontology (GR_tax).
   This ontology has associations to genes/proteins/QTL/mapsets.

 - Updates: 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 proteins, 
   EnsEMBL genes, QTL, genes.


Protein Database:
****************

The Gramene protein database now provides curated information on SP-Trembl
entries from family Poaceae (Grasses)

The protein database includes new and updated information on 67,647 gene 
products drawn from SwissProt (1874) and SP-TREMBL (65,773). These proteins are
annotated using Pfam, Prosite, TMHMM (for transmembrane domains), TargetP
and Predotar (plastid, mitochrondrial and secretory pathway targeting) 
and Interpro categories. A total of 49,249 gene products are associated 
with 1,477 Gene Ontology terms.


QTL Database:
************

The Gramene QTL database includes a total of 8,410 QTL identified for
numerous agronomic traits in rice, maize, barley, oat, wheat, pearl
millet, foxtail millet and wild rice. In this release, 250 newly
curated QTL, including some barley and wheat QTL integrated from
GrainGenes, have been added into the database.

A significant improvement in this release is the integration of "Trait 
Ontology" terms (TO) to define the associated traits of QTL. This will also 
allow the users to browse QTL by searching traits in the Gramene 
Ontology Database.


Gene Database: 
*************

The Gramene gene and allele database contains 1,488 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, 80 new rice phenotype related genes from recent
publications were added.


Marker DB:
*********

Because a large number of markers may be returned from a search, browsing
has now been limited to return maximum of 1000 markers. Users still have
the option of downloading the entire result set.
The marker database now contains a total of 1,308,654 markers from 17 species.
We have added clones and BAC end sequences from maize, Oryzaalta,
O. australiensis, O. brachyantha, O. glaberrima, andO. punctata. Two new
marker types have also been added: primers and gene primers.

Marker breakdown by species:

+---------------------+---------+
| Species             | Markers |
+---------------------+---------+
| Arabidopsis         | 50      |
| Barley              | 91      |
| Maize               | 448     |
| Oat                 | 124     |
| Oryza nivara        | 160,741 |
| Oryza rufipogon     | 107,537 |
| Oryza alta          | 33,879  |
| Oryza australiensis | 209,859 |
| Oryza brachyantha   | 99,179  |
| Oryza glaberrima    | 102,739 |
| Oryza punctata      | 104,484 |
| Oryza sativa        | 26,603  |
| Pearl Millet        | 463     |
| Sorghum             | 1,407   |
| Sugarcane           | 114     |
| Wheat               | 91      |
| Zea mays            | 460,845 |
+---------------------+---------+


CMap: 
****

In this release, we present five new physical maps: one from O. glaberrima 
and four from wild relatives of rice. There are also eight new QTL maps: one 
from barley, four from rice, two from tetraploid wheat (Triticum turgidum) 
and one from wheat. Five maps have had maintenance updates but are otherwise 
unchanged.

  New Physical Maps 	
 	
    * O. alta-OMAP FPC 2005
    * O. australiensis-OMAP FPC 2005
    * O. brachyantha-OMAP FPC 2005
    * O. glaberrima-OMAP FPC 2005
    * O. punctata-OMAP FPC 2005

  New QTL Maps	

    * Barley-NCSL Zhed/ND//Fos QTL 2003
    * Rice-CAU IRAT109/YUEFU QTL 2004
    * Rice-JUT Akihi/IRAT109 QTL 2004
    * Rice-LSU Caiapo/IRGC103544 QTL 2004
    * Rice-MU CT9993/IR6226 QTL 2004
    * Tetraploid wheat-ICARDA Omra/T.dico QTL 2004
    * Tetraploid wheat-NDSU Langdon QTL 2002
    * Wheat-AAFCCRC Wuhan1/ Marin QTL 2003

  Maintenance Updates	

    * Maize-AGI FPC Oct 2004
    * Maize-Curated AGI FPC Oct 2004
    * Sorghum-TAMU FPC 2004
    * O. nivara-OMAP O. nivara FPC 2005
    * O. rufipogon-OMAP O. rufipogon FPC 2005

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*********************************
Chengzhi Liang, PhD
Cold Spring Harbor Laboratory
One Bungtown Rd
Cold Spring Harbor, NY 11724, USA
Phone: (516) 367-8328
Email: liang at cshl.edu
http://www.gramene.org

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