A One-Phase Parallel Algorithm for the Sequence Alignment Problem

1998 ◽  
Vol 08 (04) ◽  
pp. 515-526 ◽  
Author(s):  
Thierry Lecroq ◽  
Jean-Frederic Myoupo ◽  
David Seme
Keyword(s):  
Parallel Algorithm ◽  
Sequence Alignment ◽  
Edit Distance ◽  
Linear Array ◽  
Systolic Algorithm ◽  
Alignment Problem

This paper introduces a new linear systolic algorithm [10] for the sequence alignment problem [18]. It is made up of min(n, m) processors and computes the edit distance and the sequence alignment of two sequences Target and Source in time min(n, m) + 2.max(n, m), where n and m denote the lengths of Target and Source respectively. Its characteristics make it faster and more efficient than the previous linear array algorithm for the alignment search.

A SIMPLE OPTIMAL SYSTOLIC ALGORITHM FOR GENERATING PERMUTATIONS

1992 ◽  
Vol 02 (02n03) ◽  
pp. 231-239 ◽  
Author(s):  
SELIM G. AKL ◽  
IVAN STOJMENOVIĆ
Keyword(s):  
Parallel Algorithm ◽  
Linear Array ◽  
Constant Delay ◽  
Constant Size ◽  
Time Solution ◽  
Systolic Algorithm

We describe a simple parallel algorithm for generating all permutations of n elements. The algorithm is designed to be executed on a linear array of n processors, each having constant size memory and each being responsible for producing one element of a given permutation. There is a constant delay per permutation, leading to an O (n!) time solution. The algorithm is cost-optimal, assuming the time to output the permutations is counted.

DESIGNING A SYSTOLIC ALGORITHM FOR GENERATING WELL-FORMED PARENTHESIS STRINGS

2004 ◽  
Vol 14 (01) ◽  
pp. 83-97
Author(s):  
JONG-CHUANG TSAY
Keyword(s):  
Linear Array ◽  
Vlsi Implementation ◽  
Processor Array ◽  
Lexicographical Order ◽  
Systolic Algorithm ◽  
Left And Right ◽  
Local Connection

A parenthesis string is a string of left and right parentheses. The string is well-formed when it consists of balanced pairs of left and right parentheses. This study presents a novel systolic algorithm for generating all the well-formed parenthesis strings in lexicographical order. The algorithm is cost-optimal and is run on a linear array of processors such that each well-formed parenthesis string can be generated in three time steps. The processor array is appropriate for VLSI implementation, since it has the features of modularity, regularity, and local connection.

A PARALLEL ALGORITHM TO GENERATE N-ARY REFLECTED GRAY CODES IN A LINEAR ARRAY WITH RECONFIGURABLE BUS SYSTEM

1993 ◽  
Vol 03 (02) ◽  
pp. 157-164 ◽  
Author(s):  
P. THANGAVEL ◽  
V.P. MUTHUSWAMY
Keyword(s):  
Parallel Algorithm ◽  
Linear Array ◽  
Constant Time ◽  
Processor Array ◽  
Gray Codes ◽  
System A ◽  
Processor Arrays ◽  
Bus System

A simple parallel algorithm for generating N-ary reflected Gray codes is presented. The algorithm is derived from the pattern of N-ary reflected Gray codes. The algorithm runs on a linear processor array with a reconfigurable bus system. A reconfigurable bus system is a bus system whose configuration can be dynamically changed. Recently processor arrays with reconfigurable bus systems were used to solve many problems in constant time. There already exists experimental reconfigurable chips.

scholarly journals Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Ernesto Liñán-García ◽  
Lorena Marcela Gallegos-Araiza
Keyword(s):  
Simulated Annealing ◽  
Sequence Alignment ◽  
Simulated Annealing Algorithm ◽  
Multiple Sequence ◽  
Heating And Cooling ◽  
Dna Sequence Alignment ◽  
Alignment Problem ◽  
Simple Change ◽  
Annealing Algorithm

A new algorithm for solving sequence alignment problem is proposed, which is named SAPS (Simulated Annealing with Previous Solutions). This algorithm is based on the classical Simulated Annealing (SA). SAPS is implemented in order to obtain results of pair and multiple sequence alignment. SA is a simulation of heating and cooling of a metal to solve an optimization problem. In order to select randomly a current solution, SAPS algorithm chooses a solution from solutions that have been previously generated within the Metropolis Cycle. This simple change has led to increase the quality of the solution to the problem of aligning genomic sequences with respect to the classical Simulated Annealing algorithm. The parameters of SAPS, for certain instances, are tuned by an analytical method, and some parameters have experimentally been tuned. SAPS has generated high-quality results in comparison with the classical SA. The instances used are specific genes of the AIDS virus.

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