计算机工程2018，Vol.44Issue(3)：42-46,5.DOI:10.3969/j.issn.1000-3428.2018.03.007
多基因组索引研究及其改进序列比对算法
Research on Multi-genome Index and Its Improved Sequence Alignment Algorithm
摘要
Abstract
The current multi-genome alignment algorithm requires a lot of time and memory overhead.Multi-genome Index (MuGI) alignment algorithm is faster,but failed to take advantage of multi-genomic duplication of information.therefore,an improved MuGI index alignment algorithm is proposed,which uses the dynamic seed expansion algorithm with Single Nueleotide Polymorphism (SNP) pruning and utilizes the repeated information of multiple genomes to improve the alignment speed.At the same time,it uses on-demand indexed memory management strategy to improve the space efficiency of the algorithm.Experimental results show that the improved algorithm only needs 6 GB running memory,which can be aligned on 1 092 human genomes and the speed of 5 mismatch is about 3 times faster than MuGI algorithm.关键词
序列比对/个人基因组计划/千人基因组计划/下一代测序/多基因组算法Key words
sequence alignment/Personal Genome Project (PGP)/1 000 human genomes project/Next Generation Sequencing (NGS)/Multi-genome Index (MuGI) algorithm分类
信息技术与安全科学引用本文复制引用
何忠峭,徐云..多基因组索引研究及其改进序列比对算法[J].计算机工程,2018,44(3):42-46,5.基金项目
国家自然科学基金面上项目(61672480). （61672480）
