Matlign (Matrix alignment) is a tool to align and combine a set of nucleotide matrices and/or patterns onto a smaller and more representative set of nucleotide matrices and/or patterns. The tool was originally developed for the analyses of transcription factor binding site matrices/patterns, and was therfore designed to create only a certain maximum number of gaps on the alignment. This feature (for example, this server is limited to maximally 1 gap) allows alignments that accurately reflect the true biology of the binding sites (compared to the prevailing practices that use either unlimited number of gaps or no gaps at all). For example, nuclear receptors bind onto a element that consists two short, repeated DNA sequences (either AGAACA or AGGTCA) separated by a variable length spacer (from 3 to 6 bp). To reliably combine two nuclear receptors matrices/patterns together, one therefore should allow maximally one gap (the variable length spacer) in the alignment.
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Kankainen M and Ari Löytynoja. (2003)
MATLIGN: a motif clustering, comparison and matching tool
BMC Bioinformatics, 8, 189, 1471-2105.