Strings, sequences and, ultimately, motifs play a key role in bioinformatics. Here, a motif is a biologically relevant pattern occurring in one or more input sequences. In this chapter, first we provide a formal definition of strings, sequences, matches, repetitions and motifs. Then, we present a detailed description of approaches to motif search, based on three possible taxonomies, namely: {\em (i)} the underlying algorithms; {\em (ii)} the kinds of derived motif; {\em (iii)} the kinds of considered match. After this, we illustrate the problem of assessing motif relevance, along with the current solutions. Finally, we draw some closing remarks.

Algorithms for Strings and Sequences: Searching Motifs

Abstract

Strings, sequences and, ultimately, motifs play a key role in bioinformatics. Here, a motif is a biologically relevant pattern occurring in one or more input sequences. In this chapter, first we provide a formal definition of strings, sequences, matches, repetitions and motifs. Then, we present a detailed description of approaches to motif search, based on three possible taxonomies, namely: {\em (i)} the underlying algorithms; {\em (ii)} the kinds of derived motif; {\em (iii)} the kinds of considered match. After this, we illustrate the problem of assessing motif relevance, along with the current solutions. Finally, we draw some closing remarks.
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978-0-12-811432-2
String, Sequence, Substring, Factor, Subsequence, Occurrences, Motif, String Match, String Repetition, Motif Relevance
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/20.500.11770/290005
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