Ye Liang, Huang Xiaoqiu
Department of Computer Science, Iowa State University 226 Atanasoff Hall, Ames, IA 50011-1040, USA.
Nucleic Acids Res. 2005 Jan 7;33(1):162-70. doi: 10.1093/nar/gki159. Print 2005.
We describe a multiple alignment program named MAP2 based on a generalized pairwise global alignment algorithm for handling long, different intergenic and intragenic regions in genomic sequences. The MAP2 program produces an ordered list of local multiple alignments of similar regions among sequences, where different regions between local alignments are indicated by reporting only similar regions. We propose two similarity measures for the evaluation of the performance of MAP2 and existing multiple alignment programs. Experimental results produced by MAP2 on four real sets of orthologous genomic sequences show that MAP2 rarely missed a block of transitively similar regions and that MAP2 never produced a block of regions that are not transitively similar. Experimental results by MAP2 on six simulated data sets show that MAP2 found the boundaries between similar and different regions precisely. This feature is useful for finding conserved functional elements in genomic sequences. The MAP2 program is freely available in source code form at http://bioinformatics.iastate.edu/aat/sas.html for academic use.
我们描述了一个名为MAP2的多重比对程序，它基于一种广义的全局两两比对算法，用于处理基因组序列中长的、不同的基因间和基因内区域。MAP2程序生成序列间相似区域的局部多重比对的有序列表，其中局部比对之间的不同区域仅通过报告相似区域来表示。我们提出了两种相似性度量方法来评估MAP2和现有多重比对程序的性能。MAP2在四组真实的直系同源基因组序列上产生的实验结果表明，MAP2很少错过一组传递相似区域，并且从未产生一组非传递相似的区域。MAP2在六个模拟数据集上的实验结果表明，MAP2能精确找到相似区域和不同区域之间的边界。这一特性对于在基因组序列中寻找保守功能元件很有用。MAP2程序的源代码可从http://bioinformatics.iastate.edu/aat/sas.html免费获取，供学术使用。
