Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
J Integr Bioinform. 2022 Mar 7;19(1):20210040. doi: 10.1515/jib-2021-0040.
Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences. We show that the simple, blat-based approach has advantages over established tools in particular for genes with very large introns and applications to fragmented genome assemblies.
拼接比对是构建高质量基于同源性的蛋白质序列注释的关键步骤。外显子/内含子结构是拼接比对过程的一部分，它经常为区分基因家族的旁系同源成员提供重要信息。本文提出了一种基于外显子的拼接比对管道，特别适用于涉及编码序列逐外显子比较的应用。我们表明，对于具有非常大内含子的基因和应用于碎片化基因组组装的情况，基于 blat 的简单方法比已有工具具有优势。
