Genomic Scaffold Filling Revisited
The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) I into I', with respect to a complete reference genome G, such that the number of adjacencies between G and I' is maximized. The problem is NP-complete and APX-hard, and admits a 1.2-approximation. However, the sequence input I is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when, (1) a scaffold S is given, the missing genes X = c(G) - c(S) can only be inserted in between the contigs, and the objective is to maximize the number of adjacencies between G and the filled S' and (2) a scaffold S is given, a subset of the missing genes X' subset X = c(G) - c(S) can only be inserted in between the contigs, and the objective is still to maximize the number of adjacencies between G and the filled S''. For problem (1), we present a simple NP-completeness proof, we then present a factor-2 greedy approximation algorithm, and finally we show that the problem is FPT when each gene appears at most d times in G. For problem (2), we prove that the problem is W[1]-hard and then we present a factor-2 FPT-approximation for the case when each gene appears at most d times in G.
Computational biology
Approximation algorithms
FPT algorithms
NP- completeness
15:1-15:13
Regular Paper
Haitao
Jiang
Haitao Jiang
Chenglin
Fan
Chenglin Fan
Boting
Yang
Boting Yang
Farong
Zhong
Farong Zhong
Daming
Zhu
Daming Zhu
Binhai
Zhu
Binhai Zhu
10.4230/LIPIcs.CPM.2016.15
Creative Commons Attribution 3.0 Unported license
https://creativecommons.org/licenses/by/3.0/legalcode