MAP2: multiple alignment of syntenic genomic sequences.
MAP2: multiple alignment of syntenic genomic sequences.
复制标题
MAP2：同线性基因组序列的多重比对。
DOI：
10.1093/nar/gki159
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发表时间：
2005
期刊：
影响因子：
--
通讯作者：
Huang,Xiaoqiu
中科院分区：
文献类型：
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作者：
Ye,Liang;Huang,Xiaoqiu
我们描述了一个名为 MAP2 的多重比对程序，该程序基于广义的成对全局比对算法，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通过仅报告相似区域来指示。我们提出了两种相似性度量来评估 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 很少会错过传递相似区域的块，并且 MAP2 从未产生不传递相似区域的块。 MAP2在六个模拟数据集上的实验结果表明，MAP2精确地找到了相似区域和不同区域之间的边界。此功能对于寻找基因组序列中的保守功能元件非常有用。 MAP2 程序可在 http://bioinformatics.iastate.edu/aat/sas.html 以源代码形式免费获取，供学术使用。
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.