The barley genome (Hordeum vulgare L.) has a very repetitive nature and its content of repetitive DNA exceeds 80%. We incorporated 424 million Illumina sequenced reads (8-fold coverage of the barley genome) into an index structure that is used by Kmasker to estimate k-mer frequencies. These k-mer frequencies are used to localize and mask repeats. Accordingly Kmasker is a tool providing an automated work flow for in silico extraction of unique genomic sequences of large genomic fragments suitable for various application like primer design, fluorescence in situ hybridization (FISH) or transcription activator-like effector nucleases (TALEN).
For further details please contact: Uwe Scholz
T. Schmutzer, L. Ma, N. Pousarebani, F. Bull, N. Stein, A. Houben and U. Scholz. Kmasker - A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome Species Hordeum vulgare. Cytogenetic and Genome Research, 142(1):66-78, 2014.