Genome-wide computational approach for the prediction of duplications generating protein localization signals

Authors:
Valerio Freschi;Alessandro Bogliolo;Arcangelo Liso
Affiliations:
DiSBeF, Department of Base Sciences and Fundamentals, University of Urbino, Urbino, Italy;DiSBeF, Department of Base Sciences and Fundamentals, University of Urbino, Urbino, Italy;Department of Medical and Surgery, University of Foggia, Foggia, Italy
Venue:
Computers in Biology and Medicine
Year:
2012

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A Four Russians algorithm for regular expression pattern matching

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Introduction to Automata Theory, Languages, and Computation

Introduction to Automata Theory, Languages, and Computation

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Abstract

Investigating the possible generation of motifs accountable for aberrant protein dislocation subsequent to the rise of short tandem duplications is interesting, given the pathogenic potential of this mechanism, as demonstrated in diseases such adult myeloid leukemia (AML). In this paper we introduce a new computational method for predicting genomic points which, after hypothetical mutation events such as micro-duplications, might encode molecular patterns such as localization or export signals. The proposed framework allows to study motifs of unconstrained length defined as regular expressions at a genome-wide level, providing an in silico platform capable of analyzing the potential effect of duplications on abnormal cellular localization.