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Updated: May 28, 2026

Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
Aliya Sadeque1, Marina Barsky2, Francesco Marass1
1Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.
Abstract:
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.
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