scholarly journals Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture

2008 ◽  
Author(s):  
Xiaochun Ye ◽  
Van Hoa Nguyen ◽  
Dominique Lavenier ◽  
Dongrui Fan
Keyword(s):  
Protein Sequence ◽  
Sequence Comparison ◽  
Protein Sequence Comparison ◽  
Efficient Parallelization

scholarly journals The limits of protein sequence comparison?

2005 ◽  
Vol 15 (3) ◽  
pp. 254-260 ◽  
Author(s):  
William R Pearson ◽  
Michael L Sierk
Keyword(s):  
Protein Sequence ◽  
Sequence Comparison ◽  
Protein Sequence Comparison

scholarly journals Use of FFT in Protein Sequence Comparison under Their Binary Representations

2016 ◽  
Vol 06 (02) ◽  
pp. 33-40 ◽  
Author(s):  
Jayanta Pal ◽  
Soumen Ghosh ◽  
Bansibadan Maji ◽  
Dilip Kumar Bhattacharya
Keyword(s):  
Protein Sequence ◽  
Sequence Comparison ◽  
Protein Sequence Comparison

Protein Sequence Comparison on the Connection Machine CM-2

2018 ◽  
pp. 99-107
Author(s):  
Robert Jones ◽  
Washington Taylor ◽  
Xiru Zhang ◽  
Jill P. Mesirov ◽  
Eric Lander
Keyword(s):  
Protein Sequence ◽  
Sequence Comparison ◽  
Connection Machine ◽  
Protein Sequence Comparison

scholarly journals Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lulu Yu ◽  
Yusen Zhang ◽  
Ivan Gutman ◽  
Yongtang Shi ◽  
Matthias Dehmer
Keyword(s):  
Physicochemical Properties ◽  
Protein Sequence ◽  
Sequence Comparison ◽  
Protein Sequences ◽  
Local Dynamic ◽  
Order Information ◽  
Energy Matrix ◽  
Graph Energy ◽  
Feature Based ◽  
Protein Sequence Comparison

Abstract We develop a novel position-feature-based model for protein sequences by employing physicochemical properties of 20 amino acids and the measure of graph energy. The method puts the emphasis on sequence order information and describes local dynamic distributions of sequences, from which one can get a characteristic B-vector. Afterwards, we apply the relative entropy to the sequences representing B-vectors to measure their similarity/dissimilarity. The numerical results obtained in this study show that the proposed methods leads to meaningful results compared with competitors such as Clustal W.

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