Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Parameterized Complexity Theory (Texts in Theoretical Computer Science. An EATCS Series)
Parameterized Complexity Theory (Texts in Theoretical Computer Science. An EATCS Series)
The ExemplarBreakpointDistance for Non-trivial Genomes Cannot Be Approximated
WALCOM '09 Proceedings of the 3rd International Workshop on Algorithms and Computation
Reordering contigs of draft genomes using the Mauve Aligner
Bioinformatics
The zero exemplar distance problem
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
The approximability of the exemplar breakpoint distance problem
AAIM'06 Proceedings of the Second international conference on Algorithmic Aspects in Information and Management
Non-breaking similarity of genomes with gene repetitions
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hi-index | 0.00 |
Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, a problem on filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G was studied. The objective is to minimize the resulting genomic distance between I^{\prime } and G, where I^{\prime } is the corresponding filled scaffold. We call this problem the one-sided scaffold filling problem. In this paper, we conduct a systematic study for the scaffold filling problem under the breakpoint distance and its variants, for both unichromosomal and multichromosomal genomes (with and without gene repetitions). When the input genome contains no gene repetition (i.e., is a fragment of a permutation), we show that the two-sided scaffold filling problem (i.e., G is also incomplete) is polynomially solvable for unichromosomal genomes under the breakpoint distance and for multichromosomal genomes under the genomic (or DCJ—Double-Cut-and-Join) distance. However, when the input genome contains some repeated genes, even the one-sided scaffold filling problem becomes NP-complete when the similarity measure is the maximum number of adjacencies between two sequences. For this problem, we also present efficient constant-factor approximation algorithms: factor-2 for the general case and factor 1.33 for the one-sided case.