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Standard gene mapping software packages can be used, although it is often faster to use custom code such as QTL Reaper or the web-based eQTL mapping system GeneNetwork. GeneNetwork hosts many large eQTL mapping data sets and provide access to fast algorithms to map single loci and epistatic interactions. As is true in all QTL mapping studies ...
There is software that implements ICIM additive and epistasis mapping. Its function is: (1) implementation of mapping methods including single marker analysis, interval mapping, ICIM for additive and dominance, ICIM for digenic epistasis, selective phenotyping, etc.; (2) QTL linkage analysis more than twenty mapping populations derived from bi ...
In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering genetic associations.
The principle for QTL mapping is: 1) The likelihood can be calculated for a given set of parameters (particularly QTL effect and QTL position) given the observed data on phenotypes and marker genotypes. 2) The estimates for the parameters are those where the likelihood is highest. 3) A significance threshold can be established by permutation ...
Quantitative trait loci mapping or QTL mapping is the process of identifying genomic regions that potentially contain genes responsible for important economic, health or environmental characters. Mapping QTLs is an important activity that plant breeders and geneticists routinely use to associate potential causal genes with phenotypes of interest.
However, QTL mapping resolution is impaired by the amount of recombination assayed, a problem for species in which it is difficult to obtain large offspring. Furthermore, allele diversity is restricted to individuals originated from contrasting parents, which limit studies of allele diversity when we have a panel of individuals representing a ...
High-quality alignment engine (exhaustive mapping with substitutions and indels). More accurate and several times faster than BWA or Bowtie 1/2. Many standalone biological applications (mapper, split mapper, mappability, and other) provided. Yes Yes Yes Yes Free, GPL3 [43] 2012 Genalice MAP
Splicing quantitative trait loci (abbreviated sQTLs or splicing QTLs) are quantitative trait loci that regulate alternative splicing of pre-mRNA.They can be detected using RNA-seq data.