PyElph - a software tool for gel images analysis and phylogenetics

Abstract

BackgroundThis paper presents PyElph, a software tool which automatically extracts data from gel images, computes the molecular weights of the analyzed molecules or fragments, compares DNA patterns which result from experiments with molecular genetic markers and, also, generates phylogenetic trees computed by five clustering methods, using the information extracted from the analyzed gel image. The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface and does not depend on specific image acquisition devices like other commercial programs with similar functionalities do.ResultsPyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplification of Polymorphic DNA) and STR (Short Tandem Repeat). The similarity between the DNA sequences is computed and used to generate phylogenetic trees which are very useful for population genetics studies and taxonomic classification.ConclusionsPyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices.

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

“…The 100 bp DNA Step Ladder (Promega) and the RAPD pattern of strains LMG 4252, LMG 6133 and LMG 8820 were used as references. The matrices were created with the help of PyElph 1.4 software [15] and were assembled in Microsoft Excel. An UPGMA (Unweighted Pair Group Method with Arithmetic Mean [21]) dendrogram was constructed based on a Jaccard's similarity coefficient into FreeTree 0.9.1.50 [6].…”

Temporal variations in patterns ofEscherichia colistrain diversity and antimicrobial resistance in the migrant Egyptian vulture

“…Subsequently, the polyacrylamide gel electrophoresis (PAGE) images were analysed by PyElph software [30]. Bands across the lanes were matched based on position and number of bands, and a binary matrix, designating presence of band as ‘1’ and absence as ‘0’, was made using the software.…”

Molecular characterization of Pasteurella multocida isolates from swine lungs by Randomly Amplified Polymorphic DNA

“…The DICE coefficient was used to estimate the genetic similarity of P. multocida isolates, and a dendrogram was obtained by the method of UPGMA (unweighted pair group arithmetic average) with a Bootstrap of 100, using the program PyElph 1.4 (PAVEL & VASILE, 2012).…”