改进剪接比对以鉴定直向同源物组和多个CDS比对
Improving spliced alignment for identification of ortholog groups and multiple CDS alignment
摘要：
剪接比对问题（SAP）是指在未剪接的基因组序列上寻找一个剪接的RNA序列的最佳半全局比对，已被广泛应用于基因组中基因结构的预测和注释。在这里，我们重新访问它的目的是确定CDS直系同源群内的一组CDS同源基因和计算多个CDS对齐。我们引入了一个新的约束版本的拼接比对问题，连同一个算法，利用输入RNA和基因序列的外显子-内含子结构的全部信息，以计算高覆盖率的准确比对。我们展示了如何成对剪接的CDS和一个基因家族的基因序列之间的比对可以直接使用，以便clustering一组的基因家族的CDS成一组的直系同源群。我们还介绍了一个扩展的拼接比对问题，称为多拼接比对问题（MSAP），包括在同时对齐几个RNA序列的几个基因从同一个基因家族。我们开发了一个启发式算法的解决方案的问题。我们展示了如何利用多个剪接的同源CDS成直系同源物和密切paradigs组的聚类路线，并为建设多个CDS路线。该方法在Python中的实现可按需提供到SFA@USherbrooke.ca。关键词：剪接比对，CDS直向同源群，多重CDS比对，基因结构，基因家族。
英文摘要：
The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in genomes. Here, we re-visit it for the purpose of identifying CDS ortholog groups within a set of CDS from homologous genes and for computing multiple CDS alignments. We introduce a new constrained version of the spliced alignment problem together with an algorithm that exploits full information on the exon-intron structure of the input RNA and gene sequences in order to compute high-coverage accurate alignments. We show how pairwise spliced alignments between the CDS and the gene sequences of a gene family can be directly used in order to clusterize the set of CDS of the gene family into a set of ortholog groups. We also introduce an extension of the spliced alignment problem called Multiple Spliced Alignment Problem (MSAP) that consists in aligning simultaneously several RNA sequences on several genes from the same gene family. We develop a heuristic algorithmic solution for the problem. We show how to exploit multiple spliced alignments for the clustering of homologous CDS into ortholog and close paralog groups, and for the construction of multiple CDS alignments. An implementation of the method in Python is available on demande to SFA@USherbrooke.ca. Keywords: Spliced alignment, CDS ortholog groups, Multiple CDS alignment, Gene structure, Gene family.
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。
