Gesellschaft für Informatik e.V.

Lecture Notes in Informatics


German Conference on Bioinformatics P-136, 10-20 (2008).

Gesellschaft für Informatik, Bonn
2008


Editors

Andreas Beyer (ed.), Michael Schroeder (ed.)


Copyright © Gesellschaft für Informatik, Bonn

Contents

Resqmi - aversatile algorithm and software for resequencing microarrays

Stephan Symons , Kirstin Weber , Michael Bonin and Kay Nieselt

Abstract


Resequencing microarrays are a common tool for fast monitoring of individual genetic variations. Applications include diagnosis of genetic and infectious diseases and SNP prediction. Base calling is the crucial step in the analysis of resequencing data. All current base calling algorithms produce ambiguous calls on parts of the sequence. Therefore, proper data handling, editing and visualization as well as revised calling algorithms are generally necessary for successful data interpretation. We present a base calling algorithm that uses a model-based approach using intensity comparisons and region-wise conformance assessment, as well as an algorithm to revise uncalled positions. The calling algorithm is shown to have call rates comparable to ABACUS, the currently most commonly used method. Both algorithms combined however can considerably increase the calling rate. We also present a new open source software called ResqMi, short for Resequencing using Microarrays, which focuses on the efficient and user-friendly analysis, visual inspection and easy manual editing of resequencing microarray data. Both algorithms are implemented as plugins for ResqMi. ResqMi is available at http://www-ps.informatik.uni-tuebingen.de/resqmi


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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-226-0


Last changed 04.10.2013 18:18:59