Tabu Search Method for Determining Sequences of Amino Acids in Long Polypeptides

Genetic and Tabu search algorithms for peptide assembly problem

“…c is the last symbol of z and if z starts in position i in sequence s (i > 1), then in position i − 1 there is symbol c. If c occurs exactly once in z then it is said that sequence z results from a full digest of sequence s. It means that directly after all occurrences of symbol c the cuts have been made by the protease used in the biochemical experiment. If more than one occurrence of c is present in z then z resulted from a partial digest of s. A string is obtainable from C if there exists some c ∈ C from which it is obtainable [2,6]. Besides sequences read in the sequencing process, the biochemical experiment can also provide a number of occurrences of particular amino acids in the protein.…”

“…The Tabu search method belongs to local search methods, formally described in [2], where the general step of an iterative procedure consists in constructing next solution j from current solution i and checking whether one should stop there or perform another step. Next solution j is chosen from the set N (i) -a neighborhood of feasible solutions of current solution i.…”

“…The details of the Tabu search algorithm for peptide assembly problem have been described in [2]. The main difference between the version of the algorithm described in [2] and the one used in the current paper is the definition of the objective function.…”

“…The details of the Tabu search algorithm for peptide assembly problem have been described in [2]. The main difference between the version of the algorithm described in [2] and the one used in the current paper is the definition of the objective function. Previously it was a maximization of a sum of overlaps of peptides from multiset S (spectrum) for particular permutation, while now objective function f was redefined to minimize the Manhattan distance between 20-dimensional vectors of amino acid distributions of the obtained solution and the expected one (similarly to the objective function of the proposed Genetic algorithm).…”

Machine Learning in Bioinformatics

“…Tabu search has been also recently employed to determine sequences of aminoacids in long polypeptides [216] and to extract motifs from DNA sequences [217].…”