Manipulating multiple sequence alignments via MaM and WebMaM

Abstract

MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned genomics sequences using a variety of user identified programs, databases and/or tables. The program can extract subalignments, corresponding to these various regions of DNA to be analyzed independently or in conjunction with other elements of genomic DNA. Graphical displays further allow an assessment of sequence variation throughout these different regions of the aligned sequence, providing separate displays for their repeat, non-repeat and coding portions of genomic DNA. The program should facilitate the phylogenetic analysis and processing of different portions of genomic sequence as part of large-scale sequencing efforts. MaM source code is freely available for non-commercial use at http://compbio.cs.sfu.ca/MAM.htm; and the web interface WebMaM is hosted at http://atgc.lirmm.fr/mam.

Figure 1

MaM graphical display of divergence rate across a multiple alignment. Seventeen genomic segments each corresponding to a ∼20 kb region were aligned using Clustal W. Variation in sequence divergence was measured over 1 kb windows sliding every 100 bp. The positions of exons (marked as ‘repeats’, shown in green; whereas introns are marked as ‘unique’ and shown in red) were mapped using MaM and correspond to the morpheus gene family. Some of the exons show evidence of accelerated rates of nucleotide variation when compared with the intronic regions.