Homann Robert, Fleer David, Giegerich Robert, Rehmsmeier Marc
International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
Bioinformatics. 2009 Apr 15;25(8):1084-5. doi: 10.1093/bioinformatics/btp112. Epub 2009 Feb 26.
We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data.
我们介绍了工具mkESA,这是一个用于构建增强后缀数组(ESA)的开源程序,旨在实现低内存消耗和高实际速度。mkESA是一个用可移植的C99编写的用户友好型程序,基于深度-浅度后缀数组构建算法的并行化版本,该算法以其高速和小内存使用量而闻名。该工具可处理包含多个序列的大型FASTA文件,并根据给定的序列数据计算后缀数组和各种附加表,如LCP表(最长公共前缀)或逆后缀数组。