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Speeding Up the DIALIGN Multiple Alignment Program by Using the ‘Greedy Alignment of BIOlogical Sequences LIBrary’ (GABIOS-LIB)

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Computational Biology (JOBIM 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2066))

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Abstract

A sensitive method for multiple sequence alignment should be able to align local motifs that are contained in some but not necessarily in all of the input sequences. In addition, it should be possible to integrate various of such partial local alignments into one single multiple output alignment. This leads to the question of consistency of partial alignments. Based on a new set-theoretical definition of sequence alignment, the consistency problem is discussed theoretically, and a recently developed library of C functions for consistency calculation (GABIOSLIB) is described. GABIOS-LIB has been integrated into the DIALIGN alignment program to carry out consistency tests during the multiple alignment procedure. While the resulting alignments are exactly the same as with the previous version of DIALIGN, the running time of the program has been crucially improved. For large data sets, the new version of DIALIGN is up to 120 times faster than the old version. Availability: http://bibiserv.TechFak.Uni-Bielefeld.DE/dialign/

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Author information

Authors and Affiliations

  1. LIFAR - ABISS, Faculté des Sciences et Techniques, Université de Rouen, 76821, Mont-Saint-Aignan Cedex, France

    Saïd Abdeddaïm

  2. AVENTIS Pharma, Rainham Road South, Essex, RM10 7XS, UK

    Burkhard Morgenstern

  3. MIPS, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, 82152, Martinsried, Germany

    Burkhard Morgenstern

Authors
  1. Saïd Abdeddaïm
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  2. Burkhard Morgenstern
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Editor information

Editors and Affiliations

  1. Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier, 161 rue Ada, 34392, Montpellier Cedex 5, France

    Olivier Gascuel

  2. Laboratoire d’Algorithmique Combinatoire, Institut Pasteur, 28, rue du Dr. Roux, 75724, Paris Cedex 15, France

    Marie-France Sagot

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© 2001 Springer-Verlag Berlin Heidelberg

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Abdeddaïm, S., Morgenstern, B. (2001). Speeding Up the DIALIGN Multiple Alignment Program by Using the ‘Greedy Alignment of BIOlogical Sequences LIBrary’ (GABIOS-LIB). In: Gascuel, O., Sagot, MF. (eds) Computational Biology. JOBIM 2000. Lecture Notes in Computer Science, vol 2066. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45727-5_1

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  • DOI: https://doi.org/10.1007/3-540-45727-5_1

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  • Print ISBN: 978-3-540-42242-6

  • Online ISBN: 978-3-540-45727-5

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