BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley
BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley
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DOI：
10.1007/s11032-015-0253-1
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发表时间：
2015-01-01
影响因子：
3.1
通讯作者：
Contreras-Moreira, Bruno
中科院分区：
文献类型：
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作者：
Cantalapiedra, Carlos P.;Boudiar, Ridha;Contreras-Moreira, Bruno
BARLEYMAP管道旨在针对序列富集的遗传/物理框架绘制基因组序列和转录本，植物育种者作为主要目标用户。它报告了合并来自不同资源的结果后查询的最可能的基因组位置，以便可以利用从重新测序实验中获得的多样性。此外，该应用程序还列出了周围注释的基因和标记，便于下游分析。预先计算的标记数据集也可以创建和浏览，以方便搜索和交叉引用。性能进行评估，通过映射两套长成绩单，并通过定位广泛用于高通量基因分型大麦品种的四个标记集合的物理和遗传位置。此外，检索的基因组位置BARLEYMAP的重组近交系的人口的传统遗传图谱内的位置进行比较，产生的基因顺序的准确性为96%。这些结果揭示了目前大麦基因组学计算机模拟方法的优点和缺点。利用大麦数据的网络应用程序可在http://floresta.eead.csic.es/barleymap上获得。该管道可以为具有类似序列资源的任何物种设置，可下载功能齐全的独立版本。
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. 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.