JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences.

We describe the use of Java Pattern Finder (JaPaFi) to identify short (<100 nt) highly conserved sequences in a series of poxvirus genomes. The algorithm utilizes pattern matching to identify approximate matches appearing at least once in each member of a set of genomes; a key feature is that the genomes do not need to be aligned. The user simply specifies the genomes to search, minimum length of sequences to find and the maximum number of mismatches and indels allowed. Many of the most highly conserved segments contain poxvirus promoter elements.