DNA recombination site detection software tools | Genome annotation
Meiotic recombination is vital for maintaining the sequence diversity in human genome. Meiosis and recombination are considered the essential phases of cell division. In meiosis, the genome is divided into equal parts for sexual reproduction whereas in recombination, the diverse genomes are combined to form new combination of genetic variations. The region of chromosomes where the frequency of recombination is high is called hotspot and the region where the frequency is low recombination is referred to as coldspot. The identification of recombination spots is very essential to understand the reproduction and growth of the cells.
Screens multiple-sequence alignments for recombination. GARD can discover recombination and find nonrecombinant sequence fragments. It employs screening for nonrecombinant sequence fragments to diminish false-positive error rates in the fixed effects likelihood (FEL) phylogenetic method used for selection analysis. This tool can identify discordant phylogenetic signal l in alignments of DNA or protein sequences.
Enables analysis for intersubtype mosaicism. SimPlot consists of a program designed to plot similarity versus position. The software calculates and plots the percent identity of the query sequence to a panel of reference sequences in a sliding window, which is moved across the alignment in steps. The window and step sizes are adjustable.
Assists users in detecting natural selection and recombination in RNA or DNA sequences. omegaMap is an application based on a population genetics and molecular evolution model. The signature of natural selection is determined through the ratio dN/dS, which measures the excess of non-synonymous polymorphism to synonymous polymorphism, and the signature of recombination is established from the binding imbalance models.
Allows to work about the history of recombination events that affected a given sample of bacterial genomes. ClonalOrigin run on as comparative analysis of sequences of a sample of bacterial genomes and enables to reconstruct the recombination events that have taken place in their ancestry. It contains an algorithm which permits to perform inference under this model from sequence data alignments and demonstrates that through parallelization, the inference is conceivable for whole-genome alignments.
Finds recombination hotspots from population genetic data. SequenceLDhot is based on an approximate marginal likelihood method. It scans through a chromosomal region of interest and considers fitting a recombination hotspot at a set of possible locations. This tool considers a grid of possible hotspot positions and assesses the evidence for the presence of the hotspot at each of these positions.
Helps in finding viral recombinants. RAT is a cross-platform, Java-based application intended for high-throughput, recombination analysis of both DNA and protein multiple sequence alignments, in any one of seven different file formats. It uses the distance-based method of recombination detection. This application indicates large-scale recombination occurs in the Noroviruses. Users can employ this method to examine sequences individually using the Single-sequence viewer, or use the Auto Search option that searches for recombination given a user-defined search criterion.
Aims to determine a number of genetic parameters from mapped shotgun data obtained from diploid individuals. mlRho is based on maximum likelihood estimators for θ and sequencing error. It can serve for the estimation of the rate of recombination from the correlation between the zygosity at pairs of nucleotide positions. This tool allows users to customize parameters such as average read length, coverage and error rate.