The STRAH package provides functions to extract DNA sequence data of reference genomes, functions to search for DNA-motifs in a defined DNA-sequence or to detect short tandem repeats (STRs) of specified length, and to analyze detected STRs in the human (or chimpanzees) genome by comparing them with (translated) double strand break hotspots.
Extract a specified region of any reference genome (e.g. humans, chimpanzees, ...)
DNA-motif detection of a given DNAStringSet, a given DNA-sequence in fasta-format, or a specified region of any genome
Detection of short tandem repeats (STRs) in either one or several regions of a given species
Analysis of detected short tandem repeats (STRs) in either one or several regions of a given species
STRAH data sets:
DNA-sequence of human chromosome 6 from 1,580,213 until 1,582,559
DNA-sequence of human chromosome 6 from 1,581,473 until 1,586,032
Data of the double strand break map of Pratto et al. (2014).
Translated data of the double strand break map of Pratto et al. (2014) for the chimpanzees genome.
Heissl, A., et al. (2018) Length asymmetry and heterozygosity strongly influences the evolution of poly-A microsatellites at meiotic recombination hotspots. doi: https://doi.org/10.1101/431841
Pratto, F., et al. (2014). Recombination initiation maps of individual human genomes. Science, 346(6211).
Kuhn RM, et al. (2013) The UCSC genome browser and associated tools, Brief. Bioinform., 14, 144-161.
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