Computation of Repetitions and Regularities of Biologically Weighted Sequences

Abstract

Biological weighted sequences are used extensively in molecular biology as profiles for protein families, in the representation of binding sites and often for the representation of sequences produced by a shotgun sequencing strategy. In this paper, we address three fundamental problems in the area of biologically weighted sequences: (i) computation of repetitions, (ii) pattern matching, and (iii) computation of regularities. Our algorithms can be used as basic building blocks for more sophisticated algorithms applied on weighted sequences.

String Data Structures for Computational Molecular Biology

“…There have been published works in the scientific literature [19,5,6,54] concerning the processing of string sequences; we will refer to these works giving more emphasis to the structure presented in [54]. In [19], a set of efficient algorithms were presented for string problems developing in the computational biology area.…”

“…In [19], a set of efficient algorithms were presented for string problems developing in the computational biology area. In particular, assume that we deal with a weighted sequence X of length n and with a pattern p of length m, then (i) the occurrences of p in X can be located in O((n + m) log m) time and linear space; the solution works for both the multiplicative and the average model of probability estimation, although it can be extended also to handle the appearance of gaps; (ii) the set of repetitions and the set of covers (of length m) in the weighted sequence can be computed in O(n log m) time.…”

Linear-time computation of prefix table for weighted strings & applications

“…A great deal of research has been conducted on weighted strings for pattern matching [3,4], for computing various types of regularities [5,6,7,8], for indexing [3,9], and for alignments [10,11]. The efficiency of most of the proposed algorithms relies on the assumption of a given constant cumulative weight threshold defining the minimal probability of occurrence of factors in the weighted string.…”

Practical and Efficient Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing Technologies

“…Weighted sequences are also used to represent relatively short sequences such as binding sites, as well as long sequences such as protein families profiles [3]. Additionally they have been used to represent complete chromosome sequences that were obtained using the traditional method of whole-genome shotgun strategy [3].…”

“…Additionally they have been used to represent complete chromosome sequences that were obtained using the traditional method of whole-genome shotgun strategy [3].…”