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

Aliya Sadeque,Marina Barsky,Chris Upton,Peter Kruczkiewicz,Francesco Marass

doi:10.3390/v2091867

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.

Highlights

One of the fundamental principles of molecular evolution is that extensive sequence similarity implies homology and frequently, conservation of function [1]
Subsequent experiments on the Conserved Sequence Element (CSE) led to its classification as a promoter element in poxviruses [10], the CSE remains unusual because it is remarkably well conserved for a promoter, it is longer than the average poxvirus promoter
We have discovered, using the Java Pattern Finder (JaPaFi) program, that there are a significant number of comparable sequences in this set of genomes

Summary

Introduction

One of the fundamental principles of molecular evolution is that extensive sequence similarity implies homology and frequently, conservation of function [1]. Viruses 2010, 2 genomic information from one organism—including gene number, sequence, location, and length as well as features of the non-coding regions—is compared to that of another organism in order to gain insights about phylogeny and conserved functions [2]. In studies of non-coding regions, sequences that display high degrees of conservation are regarded as good candidates for regulating gene expression [1,3]. This point is illustrated by the discovery of the Conserved Sequence Element (CSE) in 2003 during the genome sequencing of the. Subsequent experiments on the CSE led to its classification as a promoter element in poxviruses [10], the CSE remains unusual because it is remarkably well conserved for a promoter, it is longer than the average poxvirus promoter (which is normally in the range of ~30 nts)

Methods

Results

Conclusion