文章基本信息

标题：Modular and configurable optimal sequence alignment software: Cola
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作者：Neda Zamani ; Görel Sundström ; Marc P Höppner 等
期刊名称：Source Code for Biology and Medicine
印刷版ISSN：1751-0473
电子版ISSN：1751-0473
出版年度：2014
卷号：9
期号：1
页码：12
DOI：10.1186/1751-0473-9-12
语种：English
出版社：BioMed Central
摘要：The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignment does not always reflect the patterns by which nucleotides mutate. Efficiently implemented algorithms that can be parameterised to accommodate more complex non-linear scoring schemes are thus desirable. We present Cola, alignment software that implements different optimal alignment algorithms, also allowing for scoring contiguous matches of nucleotides in a nonlinear manner. The latter places more emphasis on short, highly conserved motifs, and less on the surrounding nucleotides, which can be more diverged. To illustrate the differences, we report results from aligning 14,100 sequences from 3' untranslated regions of human genes to 25 of their mammalian counterparts, where we found that a nonlinear scoring scheme is more consistent than a linear scheme in detecting short, conserved motifs. Cola is freely available under LPGL from https://github.com/nedaz/cola .
关键词：Optimal sequence alignment ; Algorithm ; DNA ; Cola