WheatIS

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Introduction

Project Objectives

This project aims at building an International Wheat Information System to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.


Flagship Databases

Gramene

Description

Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.

The controlled vocabularies (Ontologies), currently being used include

  • Gene ontology
  • Plant ontology
  • Trait ontology
  • Environment ontology
  • and Gramene Taxonomy ontology.

The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences.


Data Contents (as in Release Notes 50 (April 2016))

  1. Triticum aestivum
    • Assembly: IWGSP1
    • Gene Annotation: WGSP1 (MIPS)
  2. Triticum urartu
    • Assembly: GCA_000347455.1
    • Gene Annotation: GCA_000347455.1 (ENA, Apr 2013)
  3. Other grass species

Features

  • Genome Assembly
  • Gene Annotation
  • Comparative Genomics
  • Variation

Tools

  • Genome Browser: Browse gene annotations & diversity data
  • Plant Ractome: Browse metabolic & regulatory pathways
  • Gramene Mart: Customized data queries
  • BLAST: Align DNA & protein sequences
  • Pathways databases: BioCyc based cellular metabolic networks for 10 plant species

Technology Used

Contact

Please use the Gramene online feedback form



TAGdb

Description

TAGdb enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.

Wheat Data Contents (as on May 2016)

  • Chinese Spring group 7 raw reads
  • 16 wheat cultivars WGS raw reads

Features

  • Input sequence alignment
  • Email notification

Technology Used

  • Perl
  • MySQL

Contact

dave.edwards(at)uwa.edu.au