HAL: a hierarchical format for storing and analyzing multiple genome alignments
HAL: a hierarchical format for storing and analyzing multiple genome alignments
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DOI：
10.1093/bioinformatics/btt128
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发表时间：
2013-05-15
期刊：
影响因子：
5.8
通讯作者：
Haussler, David
中科院分区：
文献类型：
--
作者：
Hickey, Glenn;Paten, Benedict;Haussler, David
动机：大型多基因组比对和推断的祖先基因组是分子进化比较研究的理想资源，测序和计算技术的进步使它们越来越容易获得。这些结构可以为它们所包含的所有物种亚群之间的遗传关系提供丰富的理解。当前用于存储基因组比对的格式，如XMFA和MAF，都是使用单个参考基因组进行索引或排序的，然而，这限制了可以查询有关其他物种和分支的信息。这种信息的丢失随着被比较物种的数量以及它们的系统发育距离而增加。结果：我们提出了HAL，一种压缩的、基于图的分层比对格式，用于存储多个基因组比对和祖先重建。HAL图在其包含的所有基因组上进行索引。此外，它们在系统发育上是有组织的，这允许模块化和并行地访问任意亚枝，而不会因为在其他谱系中发生的重排而分裂。HAL图形可以创建或读取与一个全面的c++ API。还提供了一组工具来执行基本操作，例如导入和导出数据、识别突变和坐标映射（lift - over）。
Motivation: Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance.Results: We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover).