Please note that eDoc will be permanently shut down in the first quarter of 2021!      Home News About Us Contact Contributors Disclaimer Privacy Policy Help FAQ

Home
Search
Quick Search
Advanced
Fulltext
Browse
Collections
Persons
My eDoc
Session History
Login
Name:
Password:
Documentation
Help
Support Wiki
Direct access to
document ID:


          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



  history
ID: 405120.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
Fast and adaptive variable order Markov chain construction
Authors:Schulz, Marcel H.; Weese, David; Rausch, Tobias; Döring, Andreas; Reinert, Knut; Vingron, Martin
Language:English
Research Context:8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings
Place of Publication:Berlin / Heidelberg
Publisher:Springer
Date of Publication (YYYY-MM-DD):2008-09-18
Title of Book:Algorithms in Bioinformatics
Start Page:306
End Page:317
Full Name of Book-Editor(s):Crandall, Keith A.; Lagergren, Jens
Title of Series:Lecture Notes in Computer Science : Subseries of Lecture Notes in Computer Science
Volume:5251
Full Name(s) of Series Editor(s):S. Istrail, P. Pevzner, and M.Waterman
Copyright:© Springer. Part of Springer Science+Business Media
Review Status:not specified
Audience:Experts Only
Abstract / Description: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.
External Publication Status:published
Document Type:InBook
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
External Affiliations:1.Department of Computer Science, Free University of Berlin, Takustr. 9, 14195 Berlin, Germany.
Identifiers:URL:http://www.springerlink.com/content/w786686m07554m...
DOI:10.1007/978-3-540-87361-7
ISBN:978-3-540-87360-0
The scope and number of records on eDoc is subject to the collection policies defined by each institute - see "info" button in the collection browse view.