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

This paper presents a method for the multiple alignment of a sequence set. The MASH algorithm uses a non-redundant database of common motifs and an 'alignment priority' criterion that depends on the length and the occurrence frequency of the patterns in the set of sequences. This user-defined criterion allows the determination of the series of the patterns to be aligned. This program is applied to a fragment of envelope gene env gp120 for 20 isolates of the immunodeficiency virus. The multiplicity of alignments obtained by modifying the criterion parameters reveals different aspects of similarity between the sequences.