An efficient algorithm for optimizing whole genome alignment with noise | Zendy

Prudence W. H. Wong | Zendy; TakWah Lam | Zendy; Ning Lü | Zendy; HingFung Ting | Zendy; SiuMing Yiu | Zendy

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An efficient algorithm for optimizing whole genome alignment with noise

Author(s) -

Prudence W. H. Wong,

TakWah Lam,

Ning Lü,

HingFung Ting,

SiuMing Yiu

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth308

Subject(s) - computer science , noise (video) , genbank , heuristic , software , source code , algorithm , genome , theoretical computer science , code (set theory) , data mining , gene , artificial intelligence , biology , set (abstract data type) , genetics , programming language , image (mathematics)

This paper is concerned with algorithms for aligning two whole genomes so as to identify regions that possibly contain conserved genes. Motivated by existing heuristic-based software tools, we initiate the study of an optimization problem that attempts to uncover conserved genes with a global concern. Another interesting feature in our formulation is the tolerance of noise, which also complicates the optimization problem. A brute-force approach takes time exponential in the noise level.

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