SAGA: Sequence alignment by genetic algorithm
SAGA: Sequence alignment by genetic algorithm
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DOI：
10.1093/nar/24.8.1515
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发表时间：
1996-04-15
影响因子：
14.9
通讯作者：
Higgins, DG
中科院分区：
文献类型：
--
作者：
Notredame, C;Higgins, DG
我们描述了一种使用遗传算法和相关软件包SAGA进行多序列比对的新方法。该方法包括以准进化的方式进化比对的群体，并逐步改善由测量多个比对质量的目标函数测量的群体的适合度。SAGA使用自动调度方案来控制22个不同操作符的使用，以组合比对或在世代之间对它们进行变异。当用来优化众所周知的配对和目标函数时，SAGA比一些广泛使用的替代软件包表现得更好。这是关于实现最佳解决方案的能力以及通过与基于已知三级结构的序列的参考比对进行比较而获得的比对的准确性。这种方法的总体吸引力是能够优化任何一个人可以发明的目标函数。
We describe a new approach to multiple sequence alignment using genetic algorithms and an associated software package called SAGA. The method involves evolving a population of alignments in a quasi evolutionary manner and gradually improving the fitness of the population as measured by an objective function which measures multiple alignment quality. SAGA uses an automatic scheduling scheme to control the usage of 22 different operators for combining alignments or mutating them between generations. When used to optimise the well known sums of pairs objective function, SAGA performs better than some of the widely used alternative packages. This is seen with respect to the ability to achieve an optimal solution and with regard to the accuracy of alignment by comparison with reference alignments based on sequences of known tertiary structure. The general attraction of the approach is the ability to optimise any objective function that one can invent.