On models of the genetic code generated by binary dichotomic algorithms

• Published in: BioSystems Vol. 128; pp. 9 - 18
• Main Authors: Gumbel, Markus, Fimmel, Elena, Danielli, Alberto, Strüngmann, Lutz
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier Ireland Ltd 01.02.2015
• Subjects: Algorithms; Computational Biology - methods; Dichotomic partition; Genetic code; Genetic Code - genetics; Models, Genetic; Ribosome; Rumer; Scan algorithm; Software; Genetic code; Dichotomic partition; Ribosome; Scan algorithm; Rumer
• ISSN: 0303-2647; 1872-8324
• DOI: 10.1016/j.biosystems.2014.12.001

In this paper we introduce the concept of a BDA-generated model of the genetic code which is based on binary dichotomic algorithms (BDAs). A BDA-generated model is based on binary dichotomic algorithms (BDAs). Such a BDA partitions the set of 64 codons into two disjoint classes of size 32 each and provides a generalization of known partitions like the Rumer dichotomy. We investigate what partitions can be generated when a set of different BDAs is applied sequentially to the set of codons. The search revealed that these models are able to generate code tables with very different numbers of classes ranging from 2 to 64. We have analyzed whether there are models that map the codons to their amino acids. A perfect matching is not possible. However, we present models that describe the standard genetic code with only few errors. There are also models that map all 64 codons uniquely to 64 classes showing that BDAs can be used to identify codons precisely. This could serve as a basis for further mathematical analysis using coding theory, for example. The hypothesis that BDAs might reflect a molecular mechanism taking place in the decoding center of the ribosome is discussed. The scan demonstrated that binary dichotomic partitions are able to model different aspects of the genetic code very well. The search was performed with our tool Beady-A. This software is freely available at http://mi.informatik.hs-mannheim.de/beady-a. It requires a JVM version 6 or higher.