Comparison of large, unfinished genomic sequences requires fast methods that are robust to misordering, misorientation, and duplications. A number of fast methods exist that can compute local similarities between such sequences, from which an optimal one-to-one correspondence might be desired. However, existing methods for computing such a correspondence are either too costly to run or are inappropriate for unfinished sequence. We propose an efficient method for refining a set of segment matches such that the resulting segments are of maximal size without non-identity overlaps. This resolved set of segments can be used in various ways to compute a similarity measure between any two large sequences, and hence can be used in alignment, matching, or tree construction algorithms for two or more sequences.
CITATION STYLE
Halpern, A. L., Huson, D. H., & Reinert, K. (2002). Segment match refinement and applications. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 2452, pp. 126–136). Springer Verlag. https://doi.org/10.1007/3-540-45784-4_10
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