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PubMed · 16241898

Structured motifs search.

Michele Morgante·Alberto Policriti·Nicola Vitacolonna·Andrea Zuccolo
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Abstract

In this paper, we describe an algorithm for the localization of structured models, i.e. sequences of (simple) motifs and distance constraints. It basically combines standard pattern matching procedures with a constraint satisfaction solver, and it has the ability, not present in similar tools, to search for partial matches. A significant feature of our approach, especially in terms of efficiency for the application context, is that the (potentially) exponentially many solutions to the considered problem are represented in compact form as a graph. Moreover, the time and space necessary to build the graph are linear in the number of occurrences of the component patterns.

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AlgorithmsBase SequenceCluster AnalysisComputational BiologyDNA Transposable ElementsGenomeInformation Storage and RetrievalModels, GeneticNumerical Analysis, Computer-AssistedPattern Recognition, AutomatedSequence AlignmentSequence Analysis, DNASoftwareJournal Article

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Michele Morgante, Alberto Policriti, Nicola Vitacolonna, Andrea Zuccolo. 2005. Structured motifs search.. https://doi.org/10.1089/cmb.2005.12.1065

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