Automated image analysis for array hybridization experiments

• Published in: Bioinformatics Vol. 17; no. 7; pp. 634 - 641
• Main Authors: Steinfath, Matthias, Wruck, Wasco, Seidel, Henrik, Lehrach, Hans, Radelof, Uwe, O’Brien, John
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.07.2001; Oxford Publishing Limited (England)
• Subjects: Algorithms; Biological and medical sciences; Computational Biology; DNA Fingerprinting; Fundamental and applied biological sciences. Psychology; General aspects; Image Interpretation, Computer-Assisted; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Probes; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - statistics & numerical data; oligonucleotides; Software; Molecular hybridization; Image analysis; Computer program; Genomics; DNA chip; Transcriptome; Bioinformatics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/17.7.634

Motivation: Image analysis is a major part of data evaluation for array hybridization experiments in molecular biology. The program presented here is designed to analyze automatically images from hybridization experiments with various arrangements: different kinds of probes (oligonucleotides or complex probes), different supports (nylon filters or glass slides), different labeling of probes (radioactively or fluorescently). The program is currently applied to oligonucleotide fingerprinting projects and complex hybridizations. The only precondition for the use of the program is that the targets are arrayed in a grid, which can be approximately transformed to an orthogonal equidistant grid by a projective mapping. Results: We demonstrate that our program can cope with the following problems: global distortion of the grid, missing of grid nodes, local deviation of the spot from its specified grid position. This is checked by different quality measures. The image analysis of oligonucleotide fingerprint experiments on an entire genetic library is used, in clustering procedures, to group related clones together. The results show that the program yields automatically generated high quality input data for follow up analysis such as clustering procedures. Availability: The executable files will be available upon request for academics. Contact: steinfat@molgen.mpg.de * To whom correspondence should be addressed.