Motalign: A Multiple Sequence Alignment Algorithm Based on a New Distance and a New Score Function

Ahmed Mokaddeml; Mourad Elloumi

doi:10.1109/DEXA.2013.43

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Motalign: A Multiple Sequence Alignment Algorithm Based on a New Distance and a New Score Function

Ahmed Mokaddeml and Mourad Elloumi

2013 24th International Workshop on Database and Expert Systems Applications, pp.81-84

08/2013

DOI: https://doi.org/10.1109/DEXA.2013.43

Abstract

Algorithm design and analysis

algorithms

alignment

Benchmark testing

Bioinformatics

complexities

Databases

multiple sequence

Muscles

progressive alignment

Proteins

In this paper, we present our new progressive alignment algorithm, called Motalign, for Multiple Sequence Alignment (MSA). Our algorithm adopts a new profile based distance [1] to compare two biological sequences and a new score function, called gPSP, to align profiles. We benchmarked our algorithm on different benchmarks. We compared the results obtained by our algorithm to those obtained by other ones, like CLUSTALW2, MUSCLE and MAFFT, by using the Column Score (CS) [2] and the Sum of Pairs Score (SPS) [2]. We obtained interesting results.

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Details

Title: Motalign: A Multiple Sequence Alignment Algorithm Based on a New Distance and a New Score Function
Creators - without role: Ahmed Mokaddeml - Tunis University
Mourad Elloumi - Centre International des Technologies de l'Environnement de Tunis
Publication Details: 2013 24th International Workshop on Database and Expert Systems Applications, pp.81-84
Publisher: IEEE
Identifiers: 9932784608331
Academic Unit: University of Bisha
Language: English
Resource Type: Conference proceeding