Mai Huijun, Lam Tak-Wah, Ting Hing-Fung
Computer Science Department, University of Hong Kong, Pokfulam road, Hong Kong, China.
BMC Genomics. 2017 May 24;18(Suppl 4):362. doi: 10.1186/s12864-017-3734-2.
The recent advancement of whole genome alignment software has made it possible to align two genomes very efficiently and with only a small sacrifice in sensitivity. Yet it becomes very slow if the extra sensitivity is needed. This paper proposes a simple but effective method to improve the sensitivity of existing whole-genome alignment software without paying much extra running time.
We have applied our method to a popular whole genome alignment tool LAST, and we called the resulting tool LASTM. Experimental results showed that LASTM could find more high quality alignments with a little extra running time. For example, when comparing human and mouse genomes, to produce the similar number of alignments with similar average length and similarity, LASTM was about three times faster than LAST. We conclude that our method can be used to improve the sensitivity, and the extra time it takes is small, and thus it is worthwhile to be implemented in existing tools.
全基因组比对软件的最新进展使得高效比对两个基因组成为可能，且在灵敏度上仅有微小牺牲。然而，如果需要额外的灵敏度，其速度会变得非常慢。本文提出一种简单但有效的方法，可在不增加太多额外运行时间的情况下提高现有全基因组比对软件的灵敏度。
我们已将我们的方法应用于一个流行的全基因组比对工具LAST，并将所得工具称为LASTM。实验结果表明，LASTM能够以略多一点的运行时间找到更多高质量比对。例如，在比较人类和小鼠基因组时，为产生数量相似、平均长度和相似度相似的比对，LASTM比LAST快约三倍。我们得出结论，我们的方法可用于提高灵敏度，且增加的时间很少，因此值得在现有工具中实施。
