On the complexity and approximation of syntenic distance

The paper studies the computational complexity and approximation algorithms for a new evolutionary distance between multi-chromosomal genomes introduced recently by Ferretti, Nadeau and Sanko . Here, a chromosome is represented as a set of genes and a genome is a collections of chromosomes. The syntenic distance between two genomes is de ned as the minimumnumber of translocations, fusions and ssions required to transform one genome into the other. We prove that computing the syntenic distance is NP-hard and give a simple approximation algorithm with performance ratio 2. For the case when an upper bound d on the syntenic distance is known, we show that an an optimal syntenic sequence can be found in O(nk +2O(d2) ) time, where n and k are the number of chromosomes in the two given genomes. Next, we show that if the set of operations for transforming a genome is signi cantly restricted, we can nevertheless nd a solution that performs at most O(logd) additional moves, where d is the numbe...

• Type: Conference
• Year: 1997
• Where: RECOMB
• Authors: Bhaskar DasGupta, Tao Jiang, Sampath Kannan, Ming Li, Z. Sweedyk
• Keywords: Approximation Algorithm, Computational Biology, Genomes, RECOMB 1997, Syntenic Distance