Melanie II – a third‐generation software package for analysis of two‐dimensional electrophoresis images: II. Algorithms

Abstract

After two generations of software systems for the analysis of two-dimensional electrophoresis (2-DE) images, a third generation of such software packages has recently emerged that combines state-of-the-art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artificial intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2-D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appel et al.; Electrophoresis 1997, 18, 2724-2734).

Proteomic changes in rat thyroarytenoid muscle induced by botulinum neurotoxin injection

“…Image analysis was performed using Melanie 4.02 (GeneBio, Geneva, Switzerland) [25][26][27]; and a previously reported analysis protocol [28]. Briefly, automatic spot detection was performed and then refined by adjustment of the primary detection parameters (number of smoothing passes, saliency of the spot feature, minimum pixel area) in conjunction with visual inspection.…”

Statistical Analysis of Gel Electrophoresis Data

“…Appel et al (1997) also use polynomial warping to perform image alignment in their gel analysis tool, Melanie II. Here, the two polynomial functions for the respective axes are determined via least squares to minimize the error distance between respective landmarks in the two images.…”

Accuracy of two-dimensional electrophoresis for target discovery in human colorectal cancer

“…2 Several strategies have been developed for gene expression differential display, including serial analysis of gene expression (SAGE), 21 expressed sequence tag sequencing (EST), 20 microarray analysis 49 and RNA arbitrarily primed-PCR. 24 However, proteins are mainly responsible for tumor phenotype, and the genetic code cannot always indicate which proteins are expressed, in what quantity, and in what form.…”

“…Protein synthetic maps of both the normal left colonic mucosa and the corresponding adenocarcinoma were drawn using the Melanie 3.0 software. 20 Nine hundred and twenty-three spots could be matched between the normal and tumoral synthetic maps. Comparison of these 923 paired spots revealed that the difference in the expression of 337 polypeptides (35.5%) was superior to two-fold ( Figure 6).…”