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  1. Transactions on Computational Biology and Bioinformatics (TCBB)
  2. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 2
  3. Issue 1, January 2005
  4. Multiseed Lossless Filtration
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IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 13
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 12
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 11
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 10
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 9
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 8
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 7
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 6
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 5
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 4
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 3
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 2
Issue 4, October 2005
Issue 3, July 2005
Issue 2, April 2005
Issue 1, January 2005
Guest Editorial: WABI Special Section Part II
A New Distance for High Level RNA Secondary Structure Comparison
Topological Rearrangements and Local Search Method for Tandem Duplication Trees
Optimizing Multiple Seeds for Protein Homology Search
Editorial-State of the Transaction
Bases of Motifs for Generating Repeated Patterns with Wild Cards
Multiseed Lossless Filtration
Text Mining Biomedical Literature for Discovering Gene-to-Gene Relationships: A Comparative Study of Algorithms
2004 Reviewers List
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) : Volume 1

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Multiseed Lossless Filtration

Content Provider ACM Digital Library
Author Noe, Laurent Kucherov, Gregory Roytberg, Mikhail
Abstract We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Kärkkäinen [1]. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.
Starting Page 51
Ending Page 61
Page Count 11
File Format PDF
ISSN 15455963
DOI 10.1109/TCBB.2005.12
Volume Number 2
Issue Number 1
Journal IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language English
Publisher Association for Computing Machinery (ACM)
Publisher Date 2005-01-01
Access Restriction One Nation One Subscription (ONOS)
Subject Keyword Index Terms- Filtration, string matching, gapped seed, gapped q-gram, local alignment, sequence similarity, seed family, multiple spaced seeds, dynamic programming, EST, oligonucleotide selection.
Content Type Text
Resource Type Article
Subject Genetics Biotechnology Applied Mathematics
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