Consensus Server determines consensus patterns in unaligned sequences. The algorithm is based on a matrix representation of a consensus pattern.
Gerald Hertz (gzhertz AT alum.mit.edu), Stormo Laboratory
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Bioinformatics. 1999 Jul-Aug;15(7-8):563-77.
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
Hertz GZ, Stormo GD.