通过直接比较压缩文本索引来比较DNA序列集合
Comparing DNA sequence collections by direct comparison of compressed text indexes
摘要：
流行的序列比对工具如BWA基于Burrows-Wheeler变换（BWT）将参考基因组转换为索引数据结构，由此可以快速确定与各个查询序列的匹配。然而，对查询序列本身进行索引的实用性仍然相对未被探索。在这里，我们表明，两个序列集合的所有对所有的比较可以从每个集合的BWT计算，BWT完全保存在外部存储器中，即在磁盘上，而不是在RAM中。作为这种技术的应用，我们表明，转录组和基因组读数的BWT可以进行比较，以获得与更标准的基于参考的方法的结果具有高度重叠的剪接点的无参考预测。构建和比较大型基因组数据集的BWT的代码可在http://beetl.github.com/BEETL/作为BEETL库的一部分获得。
英文摘要：
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the utility of also indexing the query sequences themselves remains relatively unexplored. Here we show that an all-against-all comparison of two sequence collections can be computed from the BWT of each collection with the BWTs held entirely in external memory, i.e. on disk and not in RAM. As an application of this technique, we show that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions of splice junctions that have high overlap with results from more standard reference-based methods. Code to construct and compare the BWT of large genomic data sets is available at http://beetl.github.com/BEETL/ as part of the BEETL library.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
