AC-DIAMOND v1：加速大规模 DNA-蛋白质比对。
AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.
机构信息
Department of Computer Science, University of Hong Kong, Hong Kong.
L3 Bioinformatics Limited, Hong Kong.
出版信息
Bioinformatics. 2018 Nov 1;34(21):3744-3746. doi: 10.1093/bioinformatics/bty391.
SUMMARY
AC-DIAMOND (v1) is a DNA-protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed-up the matching between query and reference sequences; second, adopting a compact form of dynamic programing to fully utilize the parallelism of the SIMD capability.
AVAILABILITY AND IMPLEMENTATION
Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
AC-DIAMOND(v1) 是一款 DNA-蛋白质序列比对工具，旨在解决将大量读取序列或重叠群比对到蛋白质数据库时的效率挑战。与之前最有效的 DIAMOND 方法相比，AC-DIAMOND 的速度提高了 6 到 7 倍，同时保持了相似的灵敏度。这种改进源于两个方面：首先，使用具有自适应长度的压缩种子索引来加速查询和参考序列之间的匹配；其次，采用紧凑形式的动态编程来充分利用 SIMD 能力的并行性。
可用性和实现
软件源代码和二进制文件可在 https://github.com/Maihj/AC-DIAMOND/ 上获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
Zotero 插件