Development of Chi Sequence Analysis System on the G-Language Genome Analysis Environment

Abstract

The Chi sequence in Escherichia coli is a GT-rich octamer (5’ GCTGGTGG 3’) that acts as a signal sequence for a recombinase, RecBCD (Exonuclease V) [2]. Homologous recombination promoted by cis-acting sequence element is a widely conserved mechanism in eubacteria, and although the signal sequences differ among species, Chi analogues are identified in certain species whose complete genomes are available. As more and more complete genomes of bacteria become available at an increasing rate, it has been needed to systemize a set of analyses for higher efficiency to cope with the increasing amount of data. We have developed the Chi Sequence Analysis System on the G-language Genome Analysis Environment to analyze Chi sequences and other oligomers efficiently independent of the formats of genome databases and regardless of the types of oligomers and species. G-language Genome Analysis Environment (G-language GAE) is a generic platform for the bioinformatics analysis and software development [1]. Analysis programs can be systemized into a cascade of analyses on G-language GAE with multiple user interfaces, therefore once a set of analyses is systemized, the set of analyses can be applied to different genomes simply by a few mouse clicks from the graphical user interface.