Information theory applications for biological sequence analysis
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This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles.Abstract:
Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.read more
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Journal ArticleDOI
Alignment-free sequence comparison: benefits, applications, and tools
TL;DR: This work provides a guide to the currently available alignment-free sequence analysis tools and addresses questions about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research.
Journal ArticleDOI
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.
Jeffrey R. Wagner,Christopher T. Lee,Jacob D. Durrant,Robert D. Malmstrom,Victoria A. Feher,Rommie E. Amaro +5 more
TL;DR: Algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations are reviewed, tools that assess the druggability of these pockets are described, and how Markov state models and topology analyses provide insight into the relationship between protein dynamics andallosteric drug binding are discussed.
Journal ArticleDOI
A Tutorial for Information Theory in Neuroscience
TL;DR: This article walks through the mathematics of information theory along with common logistical problems associated with data type, data binning, data quantity requirements, bias, and significance testing, and provides a free MATLAB software package that can be applied to a wide range of data from neuroscience experiments, as well as from other fields of study.
Journal ArticleDOI
Benchmarking of alignment-free sequence comparison methods.
Andrzej Zielezinski,Hani Z. Girgis,Guillaume Bernard,Chris-André Leimeister,Kujin Tang,Thomas Dencker,Anna Katharina Lau,Sophie Röhling,Jae Jin Choi,Jae Jin Choi,Michael S. Waterman,Michael S. Waterman,Matteo Comin,Sung-Hou Kim,Sung-Hou Kim,Susana Vinga,Jonas S. Almeida,Cheong Xin Chan,Benjamin T James,Fengzhu Sun,Fengzhu Sun,Burkhard Morgenstern,Wojciech M. Karlowski +22 more
TL;DR: This work describes 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events.
Journal ArticleDOI
Alignment-Free Sequence Analysis and Applications
Jie Ren,Xin Bai,Xin Bai,Yang Young Lu,Kujin Tang,Ying Wang,Gesine Reinert,Fengzhu Sun,Fengzhu Sun +8 more
TL;DR: A review of word-count based approaches for alignment-free sequence analysis can be found in this article, where the authors provide an updated review of these applications and other related developments of word count-based approaches.
References
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Journal ArticleDOI
A mathematical theory of communication
TL;DR: This final installment of the paper considers the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now.
Book
Elements of information theory
Thomas M. Cover,Joy A. Thomas +1 more
TL;DR: The author examines the role of entropy, inequality, and randomness in the design of codes and the construction of codes in the rapidly changing environment.