BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley
Cantalapiedra CP, Boudiar R, Casas AM, Igartua E, Contreras-Moreira B (2014) BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Molecular Breeding, 35:13
The BARLEYMAP pipeline was designed to map both genomic sequences and transcripts against sequence-enriched genetic/physical frameworks, with plant breeders as the main target users. It reports the most probable genomic locations of
queries after merging results from different resources, so that diversity obtained from re-sequencing experiments can be exploited. In addition, the application lists surrounding annotated genes and markers, facilitating downstream analyses. Precomputed marker datasets can also be created and browsed to facilitate searches and cross-referencing. Performance is evaluated by mapping two sets of long transcripts and by locating the physical and genetic positions of four marker collections widely used for high-throughput genotyping of barley cultivars. In addition, genome positions retrieved by BARLEYMAP are compared to positions within a conventional genetic map for a population of recombinant inbred lines (RIL), yielding a gene order accuracy of 96%. These results reveal advantages and drawbacks of current in-silico approaches for barley genomics. A web application to make use of barley data is available at http://floresta.eead.csic.es/barleymap. The pipeline can be set up for any species with similar sequence resources, for which a fully-functional standalone version is available for download.
The BARLEYMAP pipeline was designed to map both genomic sequences and transcripts against sequence-enriched genetic/physical frameworks, with plant breeders as the main target users. It reports the most probable genomic locations of
queries after merging results from different resources, so that diversity obtained from re-sequencing experiments can be exploited. In addition, the application lists surrounding annotated genes and markers, facilitating downstream analyses. Precomputed marker datasets can also be created and browsed to facilitate searches and cross-referencing. Performance is evaluated by mapping two sets of long transcripts and by locating the physical and genetic positions of four marker collections widely used for high-throughput genotyping of barley cultivars. In addition, genome positions retrieved by BARLEYMAP are compared to positions within a conventional genetic map for a population of recombinant inbred lines (RIL), yielding a gene order accuracy of 96%. These results reveal advantages and drawbacks of current in-silico approaches for barley genomics. A web application to make use of barley data is available at http://floresta.eead.csic.es/barleymap. The pipeline can be set up for any species with similar sequence resources, for which a fully-functional standalone version is available for download.