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Título

BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley

Autor Pérez Cantalapiedra, Carlos ; Boudiar, Ridha ; Casas Cendoya, Ana María ; Igartua Arregui, Ernesto ; Contreras-Moreira, Bruno
Palabras clave Barley
Marker
Genetic and physical maps
Genotyping-by-sequencing
Gene annotation
Sequence mapping
Fecha de publicación ene-2015
EditorSpringer
Citación Cantalapiedra CP, Boudiar R, Casas AM, Igartua E, Contreras-Moreira B. BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Molecular Breeding 35: 13 (2015)
ResumenThe 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. Pre-computed 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, 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.
Descripción 25 Pags.- 2 Tabls. The definitive version is available at: http://link.springer.com/journal/11032
Versión del editorhttp://dx.doi.org/10.1007/s11032-015-0253-1
URI http://hdl.handle.net/10261/110094
DOI10.1007/s11032-015-0253-1
ISSN1380-3743
E-ISSN1572-9788
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