MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences |
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| Authors: | Chappey C; Danckaert A; Dessen P; Hazout S |
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| Institution: | Unité de Recherches Biomathétiques et Biostatistiques, INSERM U263, Université Paris 7, 2 place Jussieu, 75251 Paris Cedex 05
1Laboratoire de Biochimie, Ecole Polytechnique 91128 Palaiseau, France |
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| Abstract: | This paper presents a method for the multiple alignment of asequence set. The MASH algorithm uses a non-redundant databaseof common motifs and an ‘alignment priority’ criterionthat depends on the length and the occurrence frequency of thepatterns in the set of sequences. This user-defined criterionallows the determination of the series of the patterns to bealigned. This program is applied to a fragment of envelope geneenv gp120 for 20 isolates of the immunodeficiency virus. Themultiplicity of alignments obtained by modifying the criterionparameters reveals different aspects of similarity between thesequences.
Received on June 4, 1990; accepted on December 14, 1990 |
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