Automatic analysis of agarose gel images

• Published in: Bioinformatics 2001-11, Vol.17 (11), p.1084-1089
• Main Authors: Umesh Adiga, P. S., Bhomra, A., Turri, M. G., Nicod, A., Datta, S. R., Jeavons, P., Mott, R., Flint, J.
• Format: Article
• Language: English
• Subjects: Animals; Computational Biology; DNA - genetics; DNA - isolation & purification; Electrophoresis, Agar Gel - statistics & numerical data; Genetic Markers; Image Processing, Computer-Assisted - statistics & numerical data; Polymorphism, Genetic; Sequence Analysis, DNA - statistics & numerical data; Software; Software Design
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/17.11.1084

Motivation: Automatic tools to speed up routine biological processes are very much sought after in bio-medical research. Much repetitive work in molecular biology, such as allele calling in genetic analysis, can be made semi-automatic or task specific automatic by using existing techniques from computer science and signal processing. Computerized analysis is reproducible and avoids various forms of human error. Semi-automatic techniques with an interactive check on the results speed up the analysis and reduce the error. Results: We have successfully implemented an image processing software package to automatically analyze agarose gel images of polymorphic DNA markers. We have obtained up to 90% accuracy for the classification of alleles in good quality images and up to 70% accuracy in average quality images. These results are obtained within a few seconds. Even after subsequent interactive checking to increase the accuracy of allele classification to 100%, the overall speed with which the data can be processed is greatly increased, compared to manual allele classification. Availability: The IDL source code of the software is available on request from [e-mail] * To whom all correspondence should be addressed.