Kuznetsov Igor B, McDuffie Michael
Cancer Research Center and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, 12144, USA.
BMC Res Notes. 2015 May 7;8:187. doi: 10.1186/s13104-015-1152-6.
Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities.
PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach.
PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.
氨基酸序列比对是计算分子生物学中主要的序列比较方法。选择最适合给定比对问题的氨基酸替换矩阵是用户必须做出的最重要决策之一。在传统的氨基酸替换矩阵中，所有元素都是固定的，其值不易调整。此外，大多数现有的氨基酸替换矩阵考虑的是氨基酸类型之间的平均（不）相似性，并未区分特定生化特性对这些（不）相似性的贡献。
PR2ALIGN是一个独立的软件程序和一个网络服务器，它提供了实现灵活的用户指定比对评分函数以及基于这些序列生化特性概况比较来比对氨基酸序列对的功能。与使用20×20固定氨基酸替换矩阵的传统序列比对方法不同，PR2ALIGN使用一组氨基酸的加权生化特性来测量比对残基对之间的距离，并找到最优的最小距离全局比对。用户可以提供任意数量的氨基酸特性，并为每个特性指定一个权重。给定特性的权重越高，该特性对最终比对的影响就越大。我们表明，在许多情况下，PR2ALIGN中实现的方法比传统的基于矩阵的方法产生的双序列比对质量更高。
PR2ALIGN将有助于希望通过基于氨基酸生化特性而非氨基酸替换矩阵的灵活用户指定比对评分函数来比对氨基酸序列的研究人员。据作者所知，不存在与PR2ALIGN类似的现有独立软件程序或网络服务器。该软件可从http://pr2align.rit.albany.edu免费获取。
