if so, i have developed a new algorithm and methods. more details can be found here: geltowgs.uofk.edu.

we are about to publish an article:

Abstract:

Standard protocols for Pulsed-field gel electrophoresis (PFGE) have been adopted in a global scale for molecular sub-typing, outbreak investigations and epidemiological surveys for many pathogenic bacteria. Whole genome sequencing (WGS) is playing more significant rules for the same mentioned purposes and much more. But the results of the two techniques are being compared separately; the state of art in comparing PFGE image results is based on position tolerance (bands that fall within 0.015 of running distance are considered a match regardless of DNA co-migration). For comparing WGS results; sequence alignment is used. We have developed a new method for PFGE image analysis to calculate the number of DNA fragments in each band. Availability of multiple single bands in each PFGE lane is the cornerstone of the method. Pixel densities (PDs) of single bands are used to calculate hypothetical PDs for the other bands based on the exponential correlation between DNA fragment sizes and PDs across the same lane. Truncated values of observed PDs divided by the hypothetical ones gives the mathematical parameters we named factors of co-migration (FCMs). FCMs are integer numbers represents how many different DNA fragments are accumulated in each PFGE band. Computational assessment for the availability of single bands and PFGE coverage of whole chromosomes were carried out. A simulation of PFGEs (47,626 fragment size across 2,116 chromosome sequence) has shown that single bands comprise 64.2% and 45.8% at 5% and 10% critical fragment size difference respectively. Across the 2,116 models, 61.7% were found to cover more than 99% of the whole chromosome size. . We have built online software based on our developed method that compares PFGE to numerical models of whole chromosome sequences. Our database contains digestion models for the ten bacterial species described by PulseNet international. The web application was built in C# (C-sharp) programming language while the database management system is in structured query language (Microsoft SQL server™ 2014). Database link: geltowgs.uofk.edu