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Modular and configurable optimal sequence alignment software: Cola

机译：模块化和可配置的最佳序列比对软件：Cola

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Background 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. Results 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. Conclusions Cola is freely available under LPGL from https://github.comedaz/cola webcite.
机译：背景技术最佳比对同源序列的基本挑战是定义一种评分方案，以最能反映潜在的生物学过程。使比对中的匹配总数最大化并不总是反映核苷酸突变的模式。因此，期望能够被参数化以适应更复杂的非线性评分方案的有效实施的算法。结果我们提供了可实现不同比对算法的比对软件Cola，该软件还允许以非线性方式对核苷酸的连续匹配进行评分。后者更多地侧重于短而高度保守的基序，而较少强调周围的核苷酸，后者可更多地发散。为了说明差异，我们报告了将来自人类基因3'非翻译区的14,100个序列与25个哺乳动物对应序列进行比对的结果，我们发现非线性得分方案在检测短而保守的基序方面比线性方案更为一致。结论可乐可在LPGL下从https://github.comedaz/cola webcite免费获得。

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