Rice Gene Thresher 2.0 – Mining Genes underlying QTL in Rice Genome

RiceGeneThresher 2.0

:: DESCRIPTION

RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions.

::DEVELOPER

Rice Gene Discovery Unit, Kasetsart University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jan;37(Database issue):D996-1000. doi: 10.1093/nar/gkn638.
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.
Thongjuea S, Ruanjaichon V, Bruskiewich R, Vanavichit A.

PLABQTL 20100816 – computer program to Map QTL

PLABQTL 20100816

:: DESCRIPTION

PLABQTL (PLAnt Breeding QTL analysis)is a program written for the detection of loci which affect the variation of quantitative traits. Its main purpose is to localize and characterize QTL (Quantitative
Trait Loci).

::DEVELOPER

H. Friedrich Utz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows

:: DOWNLOAD

PLABQTL

:: MORE INFORMATION

Citation

Utz and Melchinger, 1996:
PLABQTL: A program for composite interval mapping of QTL.
Journal of Agricultural Genomics 2, 1-5

FastQTL 2.184 – Fast and Efficient QTL mapper for thousands of Molecular Phenotypes

FastQTL 2.184

:: DESCRIPTION

FastQTL is a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool.

::DEVELOPER

FunPopGen lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 FastQTL

:: MORE INFORMATION

Citation

Fast and efficient QTL mapper for thousands of molecular phenotypes.
Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O.
Bioinformatics. 2015 Dec 26. pii: btv722.

R/qtl 1.36-6 – QTL Mapping Environment

R/qtl 1.36-6

:: DESCRIPTION

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R

::DEVELOPER

R/qtl team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 R/qtl

:: MORE INFORMATION

Citation

Broman KW, Wu H, Sen Ś, Churchill GA (2003)
R/qtl: QTL mapping in experimental crosses.
Bioinformatics (2003) 19 (7): 889-890.

QTL-GPR – QTL Mapping with Count Trait

QTL-GPR

:: DESCRIPTION

QTL-GPR (quantitative trait loci – Generalized Poisson Regression) is a Matlab code for QTL mapping with count trait.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

 QTL-GPR

:: MORE INFORMATION

Citation:

Genetics. 2006 Dec;174(4):2159-72. Epub 2006 Oct 8.
On the generalized poisson regression mixture model for mapping quantitative trait loci with count data.
Cui Y1, Kim DY, Zhu J.

QlicRice – Abiotic Stress Responsive QTL and Loci Interaction Channel in Rice

QlicRice

:: DESCRIPTION

QlicRice is a database and search engine designed to encompass the majority of publicly-accessible rice quantitative trait loci (QTLs) responsive to abiotic stresses and their corresponding annotated gene (TIGR/MSU) loci.

::DEVELOPER

QlicRice team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Database (Oxford). 2011 Sep 30;2011:bar037. doi: 10.1093/database/bar037.
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC.

BioMercator v4.2.1 – Genetic Maps and QTL Integration

BioMercator v4.2.1

:: DESCRIPTION

BioMercator is a standalone application for: (1) Displaying genetic maps and QTL through a graphical user interface. (2) Performing automatic compilations of several genetic maps through a projection process. (3) Computing meta-analysis of QTL detected in independent experiments.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BioMercator

:: MORE INFORMATION

Citation:

Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J.
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.
Bioinformatics. (2004) Sep 22;20(14):2321-6.

Olivier Sosnowski, Alain Charcosset and Johann Joets.
 BioMercator V3: an upgrade of genetic map compilation and QTL meta-analysis algorithms
Bioinformatics. 2012 Aug 1;28(15):2082-3. doi: 10.1093/bioinformatics/bts313.

QMSIM 1.10 – Qtl and Marker SIMulator

QMSIM 1.10

:: DESCRIPTION

QMSim (Qtl and Marker SIMulator) was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.

::DEVELOPER

Mehdi Sargolzaei , Flavio Schenkel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 QMSim

:: MORE INFORMATION

Citation

Sargolzaei, M. and F. S. Schenkel. 2009.
QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. doi:10.1093 /bioinformatics/btp045

QTLBIM 2.0.7 – QTL Bayesian Interval Mapping

QTLBIM 2.0.7

:: DESCRIPTION

QTLBIM (QTL Bayesian Interval Mapping), provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits.

::DEVELOPER

QTLBIM Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QTLBIM

:: MORE INFORMATION

Citation:

Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, von Smith R, Yi N.
R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.
Bioinformatics. 2007 Mar 1;23(5):641-3. Epub 2007 Jan 19.

MapChart 2.2 – Graphical Presentation of Linkage Maps and QTLs

MapChart 2.2

:: DESCRIPTION

MapChart is a Windows software for the graphical presentation of linkage maps and QTLs. These charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files.

::DEVELOPER

dr. RE (Roeland) Voorrips

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  MapChart

:: MORE INFORMATION

Citation:

Voorrips, R.E., 2002.
MapChart: Software for the graphical presentation of linkage maps and QTLs.
The Journal of Heredity 93 (1): 77-78.