GelClust: a software tool for gel electrophoresis images analysis and dendrogram generation

Sahand Khakabimamaghani; Ali Najafi; Reza Ranjbar; Monireh Raam

doi:10.1016/j.cmpb.2013.04.013

GelClust: a software tool for gel electrophoresis images analysis and dendrogram generation

Comput Methods Programs Biomed. 2013 Aug;111(2):512-8. doi: 10.1016/j.cmpb.2013.04.013. Epub 2013 May 30.

Authors

Sahand Khakabimamaghani¹, Ali Najafi, Reza Ranjbar, Monireh Raam

Affiliation

¹ Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.

PMID: 23727299
DOI: 10.1016/j.cmpb.2013.04.013

Abstract

This paper presents GelClust, a new software that is designed for processing gel electrophoresis images and generating the corresponding phylogenetic trees. Unlike the most of commercial and non-commercial related softwares, we found that GelClust is very user-friendly and guides the user from image toward dendrogram through seven simple steps. Furthermore, the software, which is implemented in C# programming language under Windows operating system, is more accurate than similar software regarding image processing and is the only software able to detect and correct gel 'smile' effects completely automatically. These claims are supported with experiments.

Keywords: Dendrogram; Gel electrophoresis images; Image processing; Phylogenetic trees; Software.

MeSH terms

Algorithms
Cluster Analysis
DNA / analysis
Electronic Data Processing
Electrophoresis, Agar Gel / methods*
Electrophoresis, Polyacrylamide Gel / methods*
Image Processing, Computer-Assisted / methods*
Phylogeny
Programming Languages
Reproducibility of Results
Software*

Substances

DNA