New Genetic Markers Differentiating IPEC and ExPEC Pathotypes—A New Approach to Genome-Wide Analysis Using a New Bioinformatics Tool

Abstract

The increasingly expanding genomic databases generate the need for new tools for their processing and further use. In the paper, a bioinformatics tool, which is a search engine of microsatellite elements—trinucleotide repeat sequences (TRS) in files of FASTA type—is presented. An innovative approach was applied in the tool, which consists of connecting—within one search engine—both mapping of TRS motifs and extracting sequences that are found between the mapped TRS motifs. Accordingly, we present hereby the tool called TRS-omix, which comprises a new engine for searching information on genomes and enables generation of sets of sequences and their number, providing the basis for making comparisons between genomes. In our paper, we showed one of the possibilities of using the software. Using TRS-omix and other IT tools, we showed that we were able to extract sets of DNA sequences that can be assigned only to the genomes of the extraintestinal pathogenic Escherichia coli strains or to the genomes of the intestinal pathogenic Escherichia coli strains, as well as providing the basis for differentiation of the genomes/strains belonging to each of these clinically essential pathotypes.

Keywords

• genetic markers
• genome-wide analysis
• data analysis
• sequence analysis