title: Kmasker--a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare.
abstract: Specific localization of large genomic fragments by fluorescence in situ hybridization (FISH) is challenging in large- genome plant species due to the high content of repetitive sequences. We report the automated work flow (Kmasker) for in silico extraction of unique genomic sequences of large genomic fragments suitable for FISH in barley. This method can be widely used for the integration of genetic and cytogenetic maps in plants and other species with large and complex genomes if the probe sequence (e.g. BACs, sequence contigs) and a low coverage (8-fold) of unassembled sequences of the species of interest are available. Kmasker has been made publicly available as a web tool at http://webblast.ipk-gatersleben.de/kmasker.
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors: T
authors: T
authors: Schmutzer
authors: L
authors: L
authors: Ma
authors: N
authors: N
authors: Pousarebani
authors: F
authors: F
authors: Bull
authors: N
authors: N
authors: Stein
authors: A
authors: A
authors: Houben
authors: U
authors: U
authors: Scholz
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics; D003198:Computer Simulation; D015342:DNA Probes; D018744:DNA, Plant / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D018628:Gene Dosage; D017343:Genes, Plant; D018745:Genome, Plant; D006238:Haploidy; D001467:Hordeum / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008957:Models, Genetic; D018749:RNA, Plant / Q000235:genetics; D012341:RNA, Ribosomal, 5S / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D015342:DNA Probes; D018744:DNA, Plant; D004275:DNA, Ribosomal; D018749:RNA, Plant; D012341:RNA, Ribosomal, 5S