STRAH: STRAH: A package to detect DNA-motifs or short tandem repeats...

In STRAH: Short Tandem Repeats Analysis of Hotspot Zones

Description

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.

STRAH functions:

getflank2

Extract a specified region of any reference genome (e.g. humans, chimpanzees, ...)

motif_detection

DNA-motif detection of a given DNAStringSet, a given DNA-sequence in fasta-format, or a specified region of any genome

STR_detection

Detection of short tandem repeats (STRs) in either one or several regions of a given species

STR_analysis

Analysis of detected short tandem repeats (STRs) in either one or several regions of a given species

STRAH data sets:

chr6_1580213_1582559

DNA-sequence of human chromosome 6 from 1,580,213 until 1,582,559

chr6_1581473_1586032

DNA-sequence of human chromosome 6 from 1,581,473 until 1,586,032

dsb_map

Data of the double strand break map of Pratto et al. (2014).

dsb_map_chimp_full

Translated data of the double strand break map of Pratto et al. (2014) for the chimpanzees genome.

Author(s)

Philipp Hermann, [e-mail] (Maintainer), Monika Heinzl, [e-mail] Angelika Heissl, Irene Tiemann-Boege, Andreas Futschik

References

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.

STRAH documentation built on May 2, 2019, 11:03 a.m.