Breakpoint identification and smoothing of array comparative genomic hybridization data

Authors:
Kees Jong;Elena Marchiori;Gerrit Meijer;A. V. D. Vaart;Bauke Ylstra
Affiliations:
Faculty of Sciences;Faculty of Sciences;VU University Medical Center, Vrije Universiteit, De Boelelaan 1117, Amsterdam 1081HV, The Netherlands;Faculty of Sciences;VU University Medical Center, Vrije Universiteit, De Boelelaan 1117, Amsterdam 1081HV, The Netherlands
Venue:
Bioinformatics
Year:
2004

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Abstract

Summary: We describe a tool, called aCGH-Smooth, for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is written in visual C++, has a user-friendly interface including a visualization of the results and user-defined parameters adapting the performance of data smoothing and breakpoint recognition. aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data. Availability: aCGH-Smooth is free for researchers at academic and non-profit institutions at http://www.few.vu.nl/~vumarray/