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New Distances for Improving Progressive Alignment Algorithm

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Advances in Computing and Information Technology

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 177))

Abstract

Distance computation between sequences is an important method to compare between biological sequences. In fact, we attribute a value to the sequences in order to estimate a percentage of similarity that can help to extract structural or functional information. Distance computation is also more important in the progressive multiple alignment algorithm. Indeed, it can influence the branching order of the sequences alignment and then the final multiple alignment. In this paper, we present new methods for distance computation in order to improve the progressive multiple alignment approach. The main difference between our distances and the other existed methods consists in the use of all the sequences of the set in the pair-wise comparison. We tested our distances on BALIBASE benchmarks and we compared with other typical distances. We obtained very good results.

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Author information

Authors and Affiliations

  1. Laboratory of Technologies of Information and Communication and Electrical Engineering (LaTICE), Higher School of Sciences and Technologies of Tunis (HSSTT), University of Tunis, Tunis, Tunisia

    Ahmed Mokaddem & Mourad Elloumi

Authors
  1. Ahmed Mokaddem
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  2. Mourad Elloumi
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Corresponding author

Correspondence to Ahmed Mokaddem .

Editor information

Editors and Affiliations

  1. , Department of Computer Science, Jackson State University, John R. Lynch Street 1400, Jackson, 39217, USA

    Natarajan Meghanathan

  2. Wireilla Net Solutions PTY Ltd, Melbourne, Australia

    Dhinaharan Nagamalai

  3. Department of Computer Science & Eng., University of Calcutta, Calcutta, 700 073, India

    Nabendu Chaki

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Mokaddem, A., Elloumi, M. (2013). New Distances for Improving Progressive Alignment Algorithm. In: Meghanathan, N., Nagamalai, D., Chaki, N. (eds) Advances in Computing and Information Technology. Advances in Intelligent Systems and Computing, vol 177. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31552-7_26

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  • DOI: https://doi.org/10.1007/978-3-642-31552-7_26

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31551-0

  • Online ISBN: 978-3-642-31552-7

  • eBook Packages: EngineeringEngineering (R0)

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