Efficient Algorithms for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis

Definitions and Algorithms in SEGID

Given a (multiple) sequence alignment, SEGID first converts it into a sequence of numbers, where each number is the alignment score of a column. (SEGID also directly accepts a sequence of numbers as input.) Then it provides three algorithms to identify conserved segments (high score substrings): 1. Longest segment (with average value lower bound): given a string of numbers and a number A, find ...

Constrained Heaviest Segments in a Number Sequence and Their Applications in Biomolecular Sequence Analysis (Working Draft)

Algorithms for the Problems of Length-Constrained Heaviest Segments

We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a sequence of n real numbers and two real parameters L and U (L 6 U), the maximum sum segment problem is to find a consecutive subsequence, called a segment, of len...

Genomic Sequence Analysis: A Case Study in Constrained Heaviest Segments (Working draft)

Methods for genomic sequence analysis have been studied for more than a decade. One line of investigation is to locate the biologically meaningful segments, like conserved regions or GC-rich regions in DNA sequences. A common approach is to assign a real number (also called scores) to each residue, and then look for the maximum-sum or maximum-average segment. In this chapter, we address a few i...

MAVG: locating non-overlapping maximum average segments in a given sequence

SUMMARY MAVG is a software tool for finding k non-overlapping maximum-average segments that are sufficiently long in a given sequence of real numbers, for any k > 0. It has applications in several areas of biomolecular sequence analysis including locating GC-rich regions and CpG islands in a genomic sequence, and annotating multiple sequence alignments. AVAILABILITY http://iubio.bio.indiana.e...