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In the field of genetic sequencing, genotyping by sequencing, also called GBS, is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies . [1] GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples. [2]
Meta-genetic programming is the proposed meta-learning technique of evolving a genetic programming system using genetic programming itself. It suggests that chromosomes, crossover, and mutation were themselves evolved, therefore like their real life counterparts should be allowed to change on their own rather than being determined by a human ...
Computational genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, [1] including both DNA and RNA sequence as well as other "post-genomic" data (i.e., experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays).
The concept was first developed by Damian Jaccoud, Andrzej Kilian, David Feinstein, and Kaiman Peng in 2001. [1] They aimed to establish a genomic DNA-polymorphism detection and quantification technique that would increase throughput when compared to more traditional methods like Amplified Fragment Length Polymorphism (AFLP), Restriction Fragment Length Polymorphism (RFLP), Simple Sequence ...
Next-generation sequencing technologies such as pyrosequencing sequence less than 250 bases in a read which limits their ability to sequence whole genomes. However, their ability to generate results in real-time and their potential to be massively scaled up makes them a viable option for sequencing small regions to perform SNP genotyping.
Distributed with BBMap. (Seal - Sequence Expression AnaLyzer - is unrelated to the SEAL distributed short-read aligner.) semisup [67] Semi-supervised mixture model: detecting SNPs with interactive effects on a quantitative trait; Sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with ...
The calculation of prior probabilities depends on available data from the genome being studied, and the type of analysis being performed. For studies where good reference data containing frequencies of known mutations is available (for example, in studying human genome data), these known frequencies of genotypes in the population can be used to estimate priors.
The selection of tag SNPs is dependent on the haplotypes present in the genome. Most sequencing technologies provide the genotypic information and not the haplotypes i.e. they provide information on the specific bases that are present but do not provide phasic information (at which specific chromosome each of the bases appear). [4]