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RAGA：基于遗传算法的RNA序列比对

RAGA: RNA sequence alignment by genetic algorithm.

作者信息

Notredame C, O'Brien E A, Higgins D G

机构信息

EMBL Outstation-The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

出版信息

Nucleic Acids Res. 1997 Nov 15;25(22):4570-80. doi: 10.1093/nar/25.22.4570.

DOI:10.1093/nar/25.22.4570
PMID:9358168
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC147093/
Abstract

We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known. To do so we developed two software packages, called RAGA and PRAGA, which use a genetic algorithm approach to optimize the alignments. RAGA is mainly an extension of SAGA, an earlier package for multiple protein sequence alignment. In PRAGA several genetic algorithms run in parallel and exchange individual solutions. This method allows us to optimize an objective function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots. We report results obtained using PRAGA on nine test cases of pairs of eukaryotic small subunit rRNA sequence (nuclear and mitochondrial).

摘要

我们描述了一种新方法，用于在其中一个同源RNA序列的二级结构已知时准确比对这两个序列。为此，我们开发了两个软件包，分别称为RAGA和PRAGA，它们使用遗传算法来优化比对。RAGA主要是SAGA的扩展，SAGA是早期用于多蛋白质序列比对的软件包。在PRAGA中，多个遗传算法并行运行并交换个体解决方案。该方法使我们能够优化一个描述RNA两两比对质量的目标函数，同时考虑一级和二级结构，包括假结。我们报告了使用PRAGA在九个真核小亚基rRNA序列对（核和线粒体）测试案例上获得的结果。

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