k-Word matches: an alignment-free sequence comparison method

k-word matches, the number of words of length k shared between two sequences, also known as the D2 statistic, are used in alignment-free sequence comparison statistic. The advantages of the use of this statistic over alignment-based methods for nucleotide and amino-acid sequence comparisons are firstly that it does not assume that homologous segments are contiguous, and secondly that the algorithm is computationally extremely fast, the runtime being proportional to the size of the sequence under scrutiny. We summarise our results to date on determing the distributional properties of the D2 statistic for a range of biologically relevant parameters and outline the directions in which the research will proceed. PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-1

Contributors: Monash University. Faculty of Information Technology. Gippsland School of Information Technology ;
Chetty, Madhu ;
Ahmad, Shandar ;
Ngom, Alioune ;
Teng, Shyh Wei ;
Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB) (3rd : 2008 : Melbourne, Australia) ;
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Rights: Copyright by Third IAPR International Conference on Pattern Recognition in Bioinformatics. All rights reserved.

k元词匹配（k-word matches）指两条序列间共享的长度为k的词的数量，亦称D2统计量（D2 statistic），被应用于无比对序列比较统计分析中。相较于基于比对的核苷酸与氨基酸序列比对方法，该统计量的优势在于：其一，无需假设同源片段是连续的；其二，该算法计算效率极高，运行时长与待分析序列的规模呈线性正比关系。我们总结了截至目前针对一系列生物学相关参数下D2统计量分布特性的研究成果，并概述了该领域未来的研究方向。相关成果收录于2008年PRIB会议论文集，获取地址：http://dx.doi.org/10.1007/978-3-540-88436-1

贡献者：莫纳什大学（Monash University）信息技术学院吉普斯兰信息技术分校；马杜·切蒂（Chetty, Madhu）；尚达尔·艾哈迈德（Ahmad, Shandar）；阿利乌内·恩戈姆（Ngom, Alioune）；史伟·滕（Teng, Shyh Wei）；第三届国际模式识别生物信息学会议（Third IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008，澳大利亚墨尔本）

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