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Chaining algorithms for multiple genome comparison. (English) Zbl 1110.68541
Summary: Given $n$ fragments from $k>2$ genomes, Myers and Miller showed how to find an optimal global chain of colinear non-overlapping fragments in $O\left(n{log}^{k}n\right)$ time and $O\left(n{log}^{k-1}n\right)$ space. For gap costs in the ${L}_{1}$-metric, we reduce the time complexity of their algorithm by a factor $\frac{{log}^{2}n}{loglogn}$ and the space complexity by a factor $logn$. For the sum-of-pairs gap cost, our algorithm improves the time complexity of their algorithm by a factor $\frac{logn}{loglogn}$. A variant of our algorithm finds all significant local chains of colinear non-overlapping fragments. These chaining algorithms can be used in a variety of problems in comparative genomics: the computation of global alignments of complete genomes, the identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements, and exon prediction.
MSC:
 68W05 Nonnumerical algorithms 92C37 Cell biology 92D10 Genetics