Volume 13 Number 1 (Jan. 2018)
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JSW 2018 Vol.13(1): 57-65 ISSN: 1796-217X
doi: 10.17706/jsw.13.1.57-65

Pro-malign: Multiple Sequence Alignment Algorithm using Approached Profile

Ahmed Mokaddem*, Amine Bel Haj, and Mourad Elloumi
Laboratory of Technologies of Information and Communication, and Electrical Engineering, University of Tunis, Tunis, Tunisia.

Abstract—In this paper, we present a new progressive multiple sequence alignment algorithm called Pro-malign. Our algorithm introduces the approached profile sequence a new definition of profile that aim to conserve similar residues in the alignment. The approached profile sequence is used to compute a new distance called approached profile distance. We present also a new score function between profiles and a new refinement algorithm. We assess our program Pro-malign on different datasets extracted from different benchmarks of protein sequences and we compare the scores obtained to other scores of the most efficient multiple sequence alignment programs.

Index Terms—Multiple sequence alignment, algorithms, refinement, profiles.

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Cite: Ahmed Mokaddem, Amine Bel Haj, and Mourad Elloumi, "Pro-malign: Multiple Sequence Alignment Algorithm using Approached Profile," Journal of Software vol. 13, no. 1, pp. 57-65, 2018.

General Information

ISSN: 1796-217X (Online)
Frequency: Monthly (2006-2019); Bimonthly (Since 2020)
Editor-in-Chief: Prof. Antanas Verikas
Executive Editor: Ms. Yoyo Y. Zhou
Abstracting/ Indexing: DBLP, EBSCO, Google Scholar, ProQuest, INSPEC, ULRICH's Periodicals Directory, WorldCat, etc
E-mail: jsw@iap.org
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