A linear-time algorithm for finding the longest segment which scores above a given threshold

Details A linear-time algorithm for finding the longest segment which scores above a given threshold A linear-time algorithm for finding the longest segment which scores above a given threshold

2005-12-04

arxiv.org/abs/cs/0512016v2

Computer Science

Data Structures and Algorithms

Scientific paper

This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in which the average of the scores is above a fixed threshold. The problem originates from molecular sequence analysis: for instance, the algorithm can be employed to identify long GC-rich regions in DNA sequences. The algorithm can also be used to trim low-quality ends of shotgun sequences in a preprocessing step of whole-genome assembly.

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