Algorithms for sorting unsigned linear genomes by the DCJ operations

作者：Jiang Haitao; Zhu Binhai^*; Zhu Daming

来源：Bioinformatics, 2011, 27(3): 311-316.

DOI：10.1093/bioinformatics/btq674

Motivation: The double cut and join operation ( abbreviated as DCJ) has been extensively used for genomic rearrangement. Although the DCJ distance between signed genomes with both linear and circular (uni- and multi-) chromosomes is well studied, the only known result for the NP-complete unsigned DCJ distance problem is an approximation algorithm for unsigned linear unichromosomal genomes. In this article, we study the problem of computing the DCJ distance on two unsigned linear multichromosomal genomes (abbreviated as UDCJ).
Results: We devise a 1.5-approximation algorithm for UDCJ by exploiting the distance formula for signed genomes. In addition, we show that UDCJ admits a weak kernel of size 2k and hence an FPT algorithm running in O(2(2k)n) time.

• 出版日期2011-2-1
• 单位山东大学