MOP-UP: an online tool for finding strain-specific primers or motifs in DNA or protein alignments

MOP-UP is a web-based application that enables efficient searching of nucleic acid or amino-acid alignments for sequences or motifs that are unique to a subset of the members represented in the alignment. This has applications in the design of assays that aim to detect particular strains or species. Since molecular-based characterisation of microbes is becoming increasingly important, MOP-UP can aid microbiologists in finding the best loci on which to base such assays. The program is accessible at: http://www.hpa.org.uk/srmd/bioinformatics/tools/mop-ups.htm.