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Diversity Tools


PICARA

To systematically integrate and summarize evidence that supports genome-wide association studies (GWAS), Gramene has designed PICARA, an analytical pipeline that allows functional annotation for a priori candidates based on the co-localization of enriched GWAS signals with integrated knowledge that pertains to the same biological phenomena.

PICARA integrates homologous functional characteristics of candidates from curated information such as known genes, QTLs, pathways, and ontologies; PICARA addresses limitations of fixed-window approaches with a dynamic measure of linkage disequilibrium (LD) block size based on local SNP distributions, and then provides probabilistic inference about functional characteristics with statistical support.

By promoting the effective and systematic integration of heterogeneous biological data and facilitating the formulation of readily testable hypotheses with strong statistical support, PICARA can help researchers deepen their understanding of basic biological processes and accelerate the application of this knowledge to the fields of plant breeding and agriculture.

SNP Query

With the SNP Query tool you can perform position-based searches for SNPs in sub-regions of the genome on one, many, or all germplasm involved in a genotype study. Results include information about loci in Gramene Genomes that overlap with your chosen SNP subset.

TASSEL

TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) is a software package for evaluating trait associations, evolutionary patterns, and calculating and graphically visualizing linkage disequilibrium. Association analysis statistics include generalized linear model (GLM) and mixed linear model (MLM) approaches. TASSEL is also capable of analyzing indels, performing various diversity statistics and principle component analysis (PCA). For more detailed information see: TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635. (2007) Bradbury, P.J., et al (PDF).

Running TASSEL

You have a few different options:

Requirements

Gramene Diversity TASSEL web-launch is configured to run with TASSEL 3.0, which requires Java 6 and Java Web Start to be installed on your machine. Please contact the TASSEL developers on the TASSEL sourceforge page if you're having any problems.

Flapjack

The Plant Bioinformatics Group at the Scottish Crops Research Institute (SCRI) have developed a tool called Flapjack for graphical genotype visualization. Gramene Diversity recommends Flapjack for viewing the resequencing-based SNP data. Diversity SNP datasets have been converted to Flapjack project files which can be downloaded from our Data Download page and loaded in to Flapjack running on your machine. For OS requirments for and downloads of Flapjack go to the Flapjack download page.

GDPC Browser

The Genomic Diversity and Phenotype Connection (GDPC) Browser is an advanced search and data management utility. The standalone Java-based GDPC Browser provides advanced users with a platform for performing complex query and data filtering steps. For much more information about GDPC middeleware and the GDPC Browser, please see the official GDPC home.