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MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences.

C Chappey1, A Danckaert, P Dessen

  • 1Unité de Recherches Biomathétiques et Biostatistiques, INSERM U263, Université, Paris, France.

Computer Applications in the Biosciences : CABIOS
|April 1, 1991
PubMed
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The MASH algorithm offers a novel method for multiple sequence alignment using common motifs and a user-defined priority criterion. This approach reveals diverse similarities within the human immunodeficiency virus envelope gene sequences.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment is crucial for understanding evolutionary relationships and functional similarities between biological sequences.
  • Existing algorithms may not adequately capture complex patterns or allow for user-guided analysis.
  • Identifying conserved regions and variations in viral gene sequences is essential for vaccine development and therapeutic strategies.

Purpose of the Study:

  • To introduce the MASH algorithm, a new method for multiple sequence alignment.
  • To demonstrate the algorithm's flexibility through a user-defined 'alignment priority' criterion.
  • To analyze sequence similarities within the human immunodeficiency virus (HIV) envelope gene (env gp120).

Main Methods:

  • The MASH algorithm utilizes a non-redundant database of common sequence motifs.

Related Experiment Videos

  • An 'alignment priority' criterion, based on pattern length and frequency, guides the alignment process.
  • The algorithm was applied to a dataset of env gp120 fragments from 20 HIV isolates.

    • Main Results:

    • The MASH algorithm successfully performed multiple alignments on the HIV env gp120 sequences.
    • Varying the alignment priority criterion parameters generated multiple distinct alignments.
    • These diverse alignments highlighted different facets of sequence similarity among the HIV isolates.

    Conclusions:

    • The MASH algorithm provides a powerful and adaptable tool for multiple sequence alignment.
    • Its user-defined criterion allows for nuanced exploration of sequence relationships.
    • The application to HIV sequences demonstrates its utility in revealing complex viral genetic similarities.