A FIRST APPROACH TO FINDING COMMON MOTIFS WITH GAPS

DOI10.1142/S0129054105003716MaRDI QIDQ5714663zbMATH OpenFDO

Authors Costas S. Iliopoulos, James A. M. McHugh, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot, Wojciech Rytter

Publication date 15 December 2005

Published in International Journal of Foundations of Computer Science (Search for Journal in Brave)

Full work available at URL http://www.stringology.org/event/2004/

zbMATH Keywords

DNAgapped motifsinferencesuffix tree

Mathematics Subject Classification ID

Searching and sorting (68P10) Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30) Nonnumerical algorithms (68W05)

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• Motif trie: an efficient text index for pattern discovery with don't cares
• Computing regularities in strings: a survey
• Indexing factors with gaps
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• Structural Analysis of Gapped Motifs of a String
• INDEXING GAPPED-FACTORS USING A TREE
• Motif matching using gapped patterns
• Extracting common motifs under the Levenshtein measure: Theory and experimentation
• \textsc{Rime}: repeat identification
• String Processing and Information Retrieval
• Finding Common Motifs with Gaps Using Finite Automata
• A cost-aggregating integer linear program for motif finding
• Finding a set of long common substrings with repeats from m input strings
• Longest \((k]\)-tuple common substrings with interval length constraints
• On the complexity of finding gapped motifs

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