Approximation algorithms for NP-hard problems
Approximation algorithms for NP-hard problems
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Chaining multiple-alignment fragments in sub-quadratic time
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Modular decomposition and transitive orientation
Discrete Mathematics - Special issue on partial ordered sets
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
On the vertex ranking problem for trapezoid, circular-arc and other graphs
Discrete Applied Mathematics
Approximation algorithms
Complexity and Approximation: Combinatorial Optimization Problems and Their Approximability Properties
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Introduction to Algorithms
On computing a longest path in a tree
Information Processing Letters
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Fast and Sensitive Alignment of Large Genomic Sequences
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
EMAGEN: an efficient approach to multiple whole genome alignment
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Linear structure of bipartite permutation graphs and the longest path problem
Information Processing Letters
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Biological sequence analyses - theory, algorithms, and applications
Biological sequence analyses - theory, algorithms, and applications
Parameterized Complexity
Parameterized Complexity and Approximation Algorithms
The Computer Journal
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In this paper, we present a simple and efficient algorithm for multiple genome sequence alignment. Sequences of Maximal Unique Matches (MUMs) are first transformed into a multi-bipartite diagram. The diagram is then converted into a Directed Acyclic Graph (DAG). Therefore, finding the alignment is reduced to finding the longest path in the DAG, which is solvable in linear time. The experiments show that the algorithm can correctly find the alignment, and runs faster than MGA and EMAGEN. In addition, our algorithm can handle the alignments with overlapping MUMs and has both weighted and unweighted options. It provides the flexibility for the alignments depending on different needs.