RESOURCESRESOURCES

Natural Variation & QTL Tool Kit

Tools and resources for researchers interested in ecotypes, accessions, natural variation and QTLs in Arabidopsis.

1001 Genomes Project

http://1001genomes.org/

Homepage of the 1001 Genomes Project for Arabidopsis thaliana, which aims to to discover the whole-genome sequence variation in 1001 strains Arabidopsis thaliana to link phenotipic diversity with genome variation.

Abstract: Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. 

Arabidopsis lyrata

http://www.phytozome.net/alyrata#A

Arabidopsis Lyrata database with BLAST tool, keyword search, and map viewer. 

AraGWAS

https://aragwas.1001genomes.org/#/

The AraGWAS Catalog is a public and manually curated database for standardised GWAS results for Arabidopsis thaliana.

This Database allows to search and filter for public GWASs, phenotypes and genes and to obtain additional meta-information. All GWASs were recomputed following a uniformed methodology to allow for comparable results.

CAPSId

http://bbc.botany.utoronto.ca/capsid/

An automated CAPS marker based genotyping system. 

dCAPS finder

http://helix.wustl.edu/dcaps/dcaps.html

Programme to design PCR primers for dCAPs markers.

From the abstract: Here we describe a web-based program, dCAPS Finder 2.0, that facilitates the design of mismatched PCR primers to create or remove a restriction endonuclease recognition site relative to the polymorphism being analyzed.

easyGWAS

https://easygwas.ethz.ch/

Perform a GWAS

Use the easyGWAS wizard to simply create a GWAS. The easy to use online wizard leads you through every single step!

 

GWAPP

https://gwapp.gmi.oeaw.ac.at/index.html#!homePage

GWAPP is a web application for genome-wide association mapping in Arabidopsis. 

From the abstract: Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.

MSQT, MULTIPLE SNP QUERY TOOL

http://msqt.weigelworld.org/

Search for SNPS between arbitrary groups of ecotypes/accessions.

From the abstract: The Multiple SNP Query Tool (MSQT) extracts SNP information from multiple sequence alignments, stores it in a database, provides a web interface to query the database and outputs SNP information in a format directly applicable for SNP-assay design.

NASC Ecotype Search

http://www.arabidopsis.info/EcoForm

Searchable database of Arabidopsis ecotypes. Search options include 'altitude' and 'phenotype.'

TAIR Ecotype Search

http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype

Searchable database of ecotypes and Arabidopsis relatives.

TAIR Polymorphism Search

http://www.arabidopsis.org/servlets/Search?action=new_search&type=polyallele

Search for SNPs and visible polymorphisms in chromosomal region of interest.