AuDeNS: A Tool for Automatic De Novo Peptide Sequencing
Authors: Sacha Baginsky, Mark Cieliebak, Wilhelm Gruissem, Torsten Kleffmann, Zsuzsanna Lipták, Matthias Müller, and Paolo Penna
Reference: Technical Report 383, ETH Zurich, Department of Computer Science, October 2002
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Abstract: We have developed and implemented a framework for de novo sequencing of peptides using tandem mass spectrometry data. It first cleans the input spectrum with a number of data cleaning algorithms (``grass mowers''), followed by a sequencing algorithm that is a modification of a dynamic programming algorithm introduced in Chen et al, 2000. In first experiments, our prototype performs well (but not better) in comparison with Sequest, a frequently used software for peptide identification with database--lookup, and Lutefisk, a de novo peptide identification tool. In this paper, we present first results in the development of an efficient de novo sequencing tool.

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