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In this paper, we discuss an efficient and effective index mechanism to do the string matching with k mismatches, by which we will find all the substrings in a target string s having at most k positions different from a pattern string r. The main idea is to transform s to a BWT-array as index, denoted as BWT(s), and search r against it. During the process, the precomputed mismatch information of r...
The planted (l, d)-motif search problem is a mathematical abstraction of the DNA functional site discovery task. In this paper, we propose a heuristic algorithm that can find planted (l, d)-signals in a given set of DNA sequences. Evaluations on simulated data sets demonstrate that the proposed algorithm outperforms current widely used motif finding algorithms. We also report the results of experiments...
The DNA fragment assembly problem is an NP-complete problem which has been solved efficiently by many metaheuristics. However, those techniques generally assemble fragments that belong to noiseless DNA sequences. But nowadays dealing with noisy instances is imperative. For that we analyse exhaustively how noiseless and noisy instances of this problem are dealt by three efficient algorithms (Problem...
This paper presents the comparison between algorithms used to find inexact motifs (transformed into a set of exact sub-sequences) in a DNA sequence. The MFA algorithm builds an automaton that searches for the set of exact sub-sequences by building a finite automaton in a similar way to the KMP algorithm. This algorithm is compared against the traditional automaton using the basic idea of the subset...
We consider the problem of identifying motifs, recurring or conserved patterns, in the sets of biological sequences. To solve this task, we present new deterministic and exact algorithms for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. The proposed algorithms (1) improve search efficiency compared to existing exact algorithms by focusing search...
Extracting motifs in the sea of DNA sequences is an intricate task but have great significance. We propose an alternative solution integrating bacterial foraging optimization (BFO) algorithm and Tabu search (TS) algorithm namely TS-BFO. We modify the original BFO via established a self-control multi-length chemotactic step mechanism, and introduce Rao metric. The experiments on real data set extracted...
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