高效多基因组比对。

Efficient multiple genome alignment.

作者信息

Höhl Michael, Kurtz Stefan, Ohlebusch Enno

机构信息

Faculty of Technology, University of Bielefeld, PO Box 10 01 31, Bielefeld D-33501, Germany.

出版信息

Bioinformatics. 2002;18 Suppl 1:S312-20. doi: 10.1093/bioinformatics/18.suppl_1.s312.

DOI:10.1093/bioinformatics/18.suppl_1.s312

PMID:12169561

Abstract

MOTIVATION

To allow a direct comparison of the genomic DNA sequences of sufficiently similar organisms, there is an urgent need for software tools that can align more than two genomic sequences.

RESULTS

We developed new algorithms and a software tool 'Multiple Genome Aligner' (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, it can align 85% percent of the complete genomes of six human adenoviruses (average length 35305 bp.) in 159 seconds. An alignment of 74% of the complete genomes of three of strains of E. coli (lengths: 5528445; 5498450; 4639221 approximately bp.) is produced in 30 minutes.

摘要

动机

为了能够直接比较足够相似生物体的基因组DNA序列，迫切需要能够比对两个以上基因组序列的软件工具。

结果

我们开发了新算法和一个名为“多基因组比对器”（简称为MGA）的软件工具，它能高效地计算大型、密切相关DNA序列的多基因组比对。例如，它能在159秒内比对六种人类腺病毒（平均长度35305碱基对）完整基因组的85%。在30分钟内可生成三株大肠杆菌（长度分别约为5528445、5498450、4639221碱基对）完整基因组74%的比对结果。