BCL::Align-Sequence alignment and fold recognition with a custom scoring function online
BCL::Align-Sequence alignment and fold recognition with a custom scoring function online
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DOI：
10.1016/j.gene.2008.06.006
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发表时间：
2008-10-01
期刊：
影响因子：
3.5
通讯作者：
Meiler, Jens
中科院分区：
文献类型：
--
作者：
Dong, Elizabeth;Smith, Jarrod;Meiler, Jens
BCL：：Align是一个多序列比对工具，它利用动态编程方法结合可定制的评分函数进行序列比对和折叠识别。评分函数是传统PAM和BLOSUM评分矩阵、PSI-BIAST输出的位置特异性评分矩阵、通过多种方法预测的二级结构、化学性质和空位罚分的加权和。通过调整权重，该方法可以针对不同序列同一性水平的折叠识别或序列比对任务进行定制。使用Monte Carlo算法来确定用于序列比对和折叠识别的优化权重集，其最准确地再现SABmark参考比对测试集。在序列比对性能的评估中，与Align-m、ClustalW、T-Coffee和MUSCLE相比，BCL：：Align在比对准确性方面排名最高（对于Twilight Zone中的序列，Cline得分为22.90）。ROC曲线分析表明BCL：：Align能够正确识别蛋白质折叠，准确率超过80%。该程序的灵活性使其能够针对特定类别的蛋白质（例如膜蛋白）或折叠家族（例如TIM-桶蛋白）进行优化。BCL：：Align可免费供学术使用，并可在http://www.meilerlab.org/上在线获取。(C)2008 Elsevier B. V.保留所有权利。
BCL::Align is a multiple sequence alignment tool that utilizes the dynamic programming method in combination with a customizable scoring function for sequence alignment and fold recognition. The scoring function is a weighted sum of the traditional PAM and BLOSUM scoring matrices, position-specific scoring matrices output by PSI-BIAST, secondary structure predicted by a variety of methods, chemical properties, and gap penalties. By adjusting the weights, the method can be tailored for fold recognition or sequence alignment tasks at different levels of sequence identity. A Monte Carlo algorithm was used to determine optimized weight sets for sequence alignment and fold recognition that most accurately reproduced the SABmark reference alignment test set. In an evaluation of sequence alignment performance, BCL::Align ranked best in alignment accuracy (Cline score of 22.90 for sequences in the Twilight Zone) when compared with Align-m, ClustalW, T-Coffee, and MUSCLE. ROC curve analysis indicates BCL::Align's ability to correctly recognize protein folds with over 80% accuracy. The flexibility of the program allows it to be optimized for specific classes of proteins (e.g. membrane proteins) or fold families (e.g. TIM-barrel proteins). BCL::Align is free for academic use and available online at http://www.meilerlab.org/. (C) 2008 Elsevier B.V. All rights reserved.