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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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