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  Fast and adaptive variable order Markov chain construction

Schulz, M. H., Weese, D., Rausch, T., Döring, A., Reinert, K., & Vingron, M. (2008). Fast and adaptive variable order Markov chain construction. In K. A. Crandall, & J. Lagergren (Eds.), Algorithms in Bioinformatics (pp. 306-317). Berlin / Heidelberg: Springer.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7F0E-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7F0F-3
Genre: Book Chapter

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 Creators:
Schulz, Marcel H.1, Author
Weese, David, Author
Rausch, Tobias2, Author              
Döring, Andreas, Author
Reinert, Knut, Author
Vingron, Martin3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479666              
3Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: Variable order Markov chains (VOMCs) are a flexible class of models that extend the well-known Markov chains. They have been applied to a variety of problems in computational biology, e.g. protein family classification. A linear time and space construction algorithm has been published in 2000 by Apostolico and Bejerano. However, neither a report of the actual running time nor an implementation of it have been published since. In this paper we use the lazy suffix tree and the enhanced suffix array to improve upon the algorithm of Apostolico and Bejerano. We introduce a new software which is orders of magnitude faster than current tools for building VOMCs, and is suitable for large scale sequence analysis.

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Language(s): eng - English
 Dates: 2008-09-18
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Degree: -

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Source 1

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Title: Algorithms in Bioinformatics
Source Genre: Book
 Creator(s):
Crandall, Keith A., Editor
Lagergren, Jens, Editor
Affiliations:
-
Publ. Info: Berlin / Heidelberg : Springer
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 306 - 317 Identifier: ISBN: 978-3-540-87360-0

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Title: Lecture Notes in Computer Science : Subseries of Lecture Notes in Computer Science
Source Genre: Series
 Creator(s):
Istrail, S., Editor
Pevzner, P., Editor
M.Waterman, and, Editor
Affiliations:
-
Publ. Info: -
Pages: - Volume / Issue: 5251 Sequence Number: - Start / End Page: - Identifier: -