Journal
BRIEFINGS IN BIOINFORMATICS
Volume 15, Issue 3, Pages 376-389Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbt068
Keywords
information theory; alignment-free; Renyi entropy; sequence analysis; chaos game representation; genomic signature
Funding
- Fundacao para a Ciencia e a Tecnologia (FCT, Portugal) [PEst-OE/EEI/LA0021/2013, PEst-OE/EME/LA0022/2011]
- project InteleGen [PTDC/DTP-FTO/1747/2012]
- project BacHBerry (FP7)
- Program Investigador FCT from FCT [IF/00653/2012]
- European Social Fund (ESF) through the Operational Program Human Potential (POPH)
- Fundação para a Ciência e a Tecnologia [PEst-OE/EME/LA0022/2011] Funding Source: FCT
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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. 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.
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