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Biological sequences as pictures – a generic two dimensional solution for iterated maps |
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| Authors: | Jonas S Almeida Susana Vinga |
| Institution: | 1. Dept Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA 2. Instituto de Engenharia de Sistemas e Computadores: Investiga??o e Desenvolvimento (INESC-ID), R. Alves Redol 9, 1000-029, Lisboa, Portugal 3. Dept Bioestatística e Informática, Faculdade de Ciências Médicas – Universidade Nova de Lisboa (FCM/UNL), Campo Mártires da Pátria 130, 1169-056, Lisboa, Portugal |
| Abstract: | BackgroundRepresenting symbolic sequences graphically using iterated maps has enjoyed an enduring popularity since it was first proposed in Jeffrey 1990 as chaos game representation (CGR). The usefulness of this representation goes beyond the convenience of a scale independent representation, it provides a variable memory length representation of transition. This includes the representation of succession with non-integer order, which comes with the promise of generalizing Markovian formalisms. The original proposal targeted genomic sequences only but since then several generalizations have been proposed, many specifically designed to handle protein data. |
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