On models of the genetic code generated by binary dichotomic algorithms
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 p...
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| Published in | BioSystems Vol. 128; pp. 9 - 18 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Ireland
Elsevier Ireland Ltd
01.02.2015
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0303-2647 1872-8324 1872-8324 |
| DOI | 10.1016/j.biosystems.2014.12.001 |
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| Abstract | 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. |
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| AbstractList | 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.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. 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. 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. |
| Author | Gumbel, Markus Danielli, Alberto Fimmel, Elena Strüngmann, Lutz |
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| Cites_doi | 10.1016/j.febslet.2013.05.009 10.1016/j.biosystems.2012.03.001 10.1016/j.jtbi.2014.08.036 10.1093/bioinformatics/btn397 10.1038/nsmb.2545 10.1016/j.jtbi.2013.07.027 10.1186/1745-6150-3-37 10.1016/S1097-2765(04)00005-X 10.1073/pnas.43.5.416 10.1016/0022-2836(68)90392-6 10.1006/jtbi.1996.0142 10.1038/nature08403 10.1002/iub.146 10.1007/BF02103132 10.1016/S0092-8674(02)01086-3 10.1016/j.jtbi.2007.07.007 10.1038/nature10913 10.1023/A:1025771327614 10.1103/PhysRevE.78.051918 10.1126/science.1060612 10.1016/j.biosystems.2014.09.012 10.1016/0305-0491(93)90122-L 10.1128/MMBR.00010-08 10.1128/MMBR.56.1.229-264.1992 10.1016/j.compbiolchem.2011.10.002 10.1016/j.jmb.2006.11.046 10.1098/rsta.2011.0387 10.1261/rna.1745910 10.1073/pnas.72.5.1909 10.1038/173318a0 10.1007/s00239-004-0176-7 10.1016/j.compbiolchem.2014.08.001 |
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| Keywords | Genetic code Dichotomic partition Ribosome Scan algorithm Rumer |
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| References | Seligmann (bib0150) Nov 2007; 249 Koonin, Novozhilov (bib0105) 2009; 61 Haig, Hurst (bib0085) 1991; 33 Seligmann (bib0090) Aug 2014; 363C Demeshkina, Jenner, Westhof, Yusupov, Yusupova (bib0035) 2013; 587 Masliah, Barraud, Allain (bib0110) 2013; 70 Voorhees, Mandal, Neubauer, Köhrer, RajBhandary, Ramakrishnan (bib0175) 2013; 20 Wong (bib0180) 1975; 72 Crick, Griffith, Orgel (bib0020) 1957; 43 Gonzalez, Giannerini, Rosa (bib0065) Nov 2008; 78 Sella, Ardell (bib0160) 2006; 63 Shaul, Berel, Benjamini, Graur (bib0165) 2010; 16 Fimmel, Danielli, Strüngmann (bib0040) 2013; 336 El Soufi, Michel (bib0170) Oct 2014; 52 Jukes, Osawa (bib0100) 1993; 106 Gamow (bib0050) 1954; 173 Arquès, Michel (bib0010) 1996; 182 Di Giulio (bib0060) 2008; 3 Demeshkina, Jenner, Westhof, Yusupov, Yusupova (bib0030) 2012; 484 Seligmann (bib0155) Oct 2014; 125C Gonzalez (bib0070) 2008 Rumer (bib0140) 1966; 167 Ogle, Murphy, Tarry, Ramakrishnan (bib0130) 2002; 111 Atkins (bib0015) 2009; 73 Michel (bib0115) Apr 2012; 37 Freeland, Wu, Keulmann (bib0045) Oct 2003; 33 Holland, Down, Pocock, Prlic, Ardelluen, James, Foisy, Dräger, Yates, Heuer, Schreiber (bib0095) Sep 2008; 24 Odersky, Spoon, Venners (bib0120) 2010 Agris, Vendeix, Graham (bib0005) 2007; 366 Osawa, Jukes, Watanabe, Muto (bib0135) 1992; 56 Crick (bib0025) 1968; 38 Ogle, Brodersen, Clemons, Tarry, Carter, Ramakrishnan (bib0125) 2001; 292 Guilloux, Jestin (bib0080) 2012; 109 Gromadski, Rodnina (bib0075) 2004; 13 Schmeing, Ramakrishnan (bib0145) 2009; 461 Giannerini, Gonzalez, Rosa (bib0055) Jun 2012; 370 Seligmann (10.1016/j.biosystems.2014.12.001_bib0090) 2014; 363C Atkins (10.1016/j.biosystems.2014.12.001_bib0015) 2009; 73 Wong (10.1016/j.biosystems.2014.12.001_bib0180) 1975; 72 Demeshkina (10.1016/j.biosystems.2014.12.001_bib0030) 2012; 484 Sella (10.1016/j.biosystems.2014.12.001_bib0160) 2006; 63 Holland (10.1016/j.biosystems.2014.12.001_bib0095) 2008; 24 Osawa (10.1016/j.biosystems.2014.12.001_bib0135) 1992; 56 Voorhees (10.1016/j.biosystems.2014.12.001_bib0175) 2013; 20 Haig (10.1016/j.biosystems.2014.12.001_bib0085) 1991; 33 Masliah (10.1016/j.biosystems.2014.12.001_bib0110) 2013; 70 Guilloux (10.1016/j.biosystems.2014.12.001_bib0080) 2012; 109 Agris (10.1016/j.biosystems.2014.12.001_bib0005) 2007; 366 Freeland (10.1016/j.biosystems.2014.12.001_bib0045) 2003; 33 Seligmann (10.1016/j.biosystems.2014.12.001_bib0155) 2014; 125C Demeshkina (10.1016/j.biosystems.2014.12.001_bib0035) 2013; 587 Michel (10.1016/j.biosystems.2014.12.001_bib0115) 2012; 37 Fimmel (10.1016/j.biosystems.2014.12.001_bib0040) 2013; 336 Ogle (10.1016/j.biosystems.2014.12.001_bib0125) 2001; 292 Giannerini (10.1016/j.biosystems.2014.12.001_bib0055) 2012; 370 Rumer (10.1016/j.biosystems.2014.12.001_bib0140) 1966; 167 Arquès (10.1016/j.biosystems.2014.12.001_bib0010) 1996; 182 El Soufi (10.1016/j.biosystems.2014.12.001_bib0170) 2014; 52 Crick (10.1016/j.biosystems.2014.12.001_bib0020) 1957; 43 Di Giulio (10.1016/j.biosystems.2014.12.001_bib0060) 2008; 3 Ogle (10.1016/j.biosystems.2014.12.001_bib0130) 2002; 111 Shaul (10.1016/j.biosystems.2014.12.001_bib0165) 2010; 16 Gamow (10.1016/j.biosystems.2014.12.001_bib0050) 1954; 173 Schmeing (10.1016/j.biosystems.2014.12.001_bib0145) 2009; 461 Gonzalez (10.1016/j.biosystems.2014.12.001_bib0070) 2008 Koonin (10.1016/j.biosystems.2014.12.001_bib0105) 2009; 61 Seligmann (10.1016/j.biosystems.2014.12.001_bib0150) 2007; 249 Crick (10.1016/j.biosystems.2014.12.001_bib0025) 1968; 38 Gonzalez (10.1016/j.biosystems.2014.12.001_bib0065) 2008; 78 Odersky (10.1016/j.biosystems.2014.12.001_bib0120) 2010 Gromadski (10.1016/j.biosystems.2014.12.001_bib0075) 2004; 13 Jukes (10.1016/j.biosystems.2014.12.001_bib0100) 1993; 106 |
| References_xml | – volume: 363C start-page: 216 year: Aug 2014 end-page: 222 ident: bib0090 article-title: Species radiation by DNA replication that systematically exchanges nucleotides? publication-title: J. Theor. Biol. – volume: 587 start-page: 1848 year: 2013 end-page: 1857 ident: bib0035 article-title: New structural insights into the decoding mechanism: translation in-delity via a G–U pair with Watson-Crick geometry publication-title: FEBS Lett. – year: 2010 ident: bib0120 article-title: Programming in Scala – volume: 16 start-page: 141 year: 2010 end-page: 153 ident: bib0165 article-title: Revisiting the operational RNA code for amino acids: ensemble attributes and their implications publication-title: RNA – volume: 109 start-page: 141 year: 2012 end-page: 144 ident: bib0080 article-title: The genetic code and its optimization for kinetic energy conservation in polypeptide chains publication-title: Biosystems – volume: 167 start-page: 1393 year: 1966 end-page: 1394 ident: bib0140 article-title: Codon systematization in the genetic code publication-title: Dokl. Akad. Nauk. SSSR – volume: 33 start-page: 457 year: Oct 2003 end-page: 477 ident: bib0045 article-title: The case for an error minimizing standard genetic code publication-title: Orig. Life Evol. Biosph. – volume: 182 start-page: 45 year: 1996 end-page: 58 ident: bib0010 article-title: A complementary circular code in the protein coding genes publication-title: J. Theor. Biol. – volume: 3 start-page: 37 year: 2008 ident: bib0060 article-title: An extension of the coevolution theory of the origin of the genetic code publication-title: Biol. Direct – volume: 461 start-page: 1234 year: 2009 end-page: 1242 ident: bib0145 article-title: What recent ribosome structures have revealed about the mechanism of translation publication-title: Nature – volume: 249 start-page: 162 year: Nov 2007 end-page: 167 ident: bib0150 article-title: Cost minimization of ribosomal frameshifts publication-title: J. Theor. Biol. – volume: 78 start-page: 051918 year: Nov 2008 ident: bib0065 article-title: Strong short-range correlations and dichotomic codon classes in coding DNA sequences publication-title: Phys. Rev. E: Stat. Nonlin. Soft Matter Phys. – volume: 13 start-page: 191 year: 2004 end-page: 200 ident: bib0075 article-title: Kinetic determinants of high-fidelity tRNA discrimination on the ribosome publication-title: Mol. Cell – volume: 292 start-page: 897 year: 2001 end-page: 902 ident: bib0125 article-title: Recognition of cognate transfer RNA by the 30s ribosomal subunit publication-title: Science – year: 2008 ident: bib0070 article-title: The mathematical structure of the genetic code publication-title: Codes of Life: The Rules of Microevolution – volume: 38 start-page: 367 year: 1968 end-page: 379 ident: bib0025 article-title: The origin of the genetic code publication-title: J. Mol. Biol. – volume: 370 start-page: 2987 year: Jun 2012 end-page: 3006 ident: bib0055 article-title: DNA, dichotomic classes and frame synchronization: a quasi-crystal framework publication-title: Philos. Trans. A: Math. Phys. Eng. Sci. – volume: 37 start-page: 24 year: Apr 2012 end-page: 37 ident: bib0115 article-title: Circular code motifs in transfer and 16s ribosomal RNAs: a possible translation code in genes publication-title: Comput. Biol. Chem. – volume: 73 start-page: 178 year: 2009 end-page: 210 ident: bib0015 article-title: A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight p-site realignment publication-title: Microbiol. Mol. Biol. Rev. – volume: 336 start-page: 221 year: 2013 end-page: 230 ident: bib0040 article-title: On dichotomic classes and bijections of the genetic code publication-title: J. Theor. Biol. – volume: 56 start-page: 229 year: 1992 end-page: 264 ident: bib0135 article-title: Recent evidence for evolution of the genetic code publication-title: Microbiol. Rev. – volume: 43 start-page: 416 year: 1957 end-page: 421 ident: bib0020 article-title: Codes without commas publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 61 start-page: 99 year: 2009 end-page: 111 ident: bib0105 article-title: Origin and evolution of the genetic code: the universal enigma publication-title: IUBMB Life – volume: 72 start-page: 1909 year: 1975 end-page: 1912 ident: bib0180 article-title: A co-evolution theory of the genetic code publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 111 start-page: 721 year: 2002 end-page: 732 ident: bib0130 article-title: Selection of tRNA by the ribosome requires a transition from an open to a closed form publication-title: Cell – volume: 366 start-page: 1 year: 2007 end-page: 13 ident: bib0005 article-title: tRNA's wobble decoding of the genome: 40 years of modification publication-title: J. Mol. Biol. – volume: 20 start-page: 641 year: 2013 end-page: 643 ident: bib0175 article-title: The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome publication-title: Nat. Struct. Mol. Biol. – volume: 173 start-page: 318 year: 1954 ident: bib0050 article-title: Possible relation between deoxyribonucleic acid and protein structures publication-title: Nature – volume: 33 start-page: 412 year: 1991 end-page: 417 ident: bib0085 article-title: A quantitative measure of error minimization in the genetic code publication-title: J. Mol. Evol. – volume: 70 start-page: 1875 year: 2013 end-page: 1895 ident: bib0110 article-title: RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence publication-title: Cell. Mol. Life Sci. – volume: 484 start-page: 256 year: 2012 end-page: 259 ident: bib0030 article-title: A new understanding of the decoding principle on the ribosome publication-title: Nature – volume: 52 start-page: 9 year: Oct 2014 end-page: 17 ident: bib0170 article-title: Circular code motifs in the ribosome decoding center publication-title: Comput. Biol. Chem. – volume: 106 start-page: 489 year: 1993 end-page: 494 ident: bib0100 article-title: Evolutionary changes in the genetic code publication-title: Comp. Biochem. Physiol. B – volume: 125C start-page: 22 year: Oct 2014 end-page: 31 ident: bib0155 article-title: Mitochondrial swinger replication: DNA replication systematically exchanging nucleotides and short 16s ribosomal DNA swinger inserts publication-title: Biosystems – volume: 63 start-page: 297 year: 2006 end-page: 313 ident: bib0160 article-title: The coevolution of genes and genetic codes: Crick's frozen accident revisited publication-title: J. Mol. Evol. – volume: 24 start-page: 2096 year: Sep 2008 end-page: 2097 ident: bib0095 article-title: BioJava: an open-source framework for bioinformatics publication-title: Bioinformatics – volume: 587 start-page: 1848 issue: 13 year: 2013 ident: 10.1016/j.biosystems.2014.12.001_bib0035 article-title: New structural insights into the decoding mechanism: translation in-delity via a G–U pair with Watson-Crick geometry publication-title: FEBS Lett. doi: 10.1016/j.febslet.2013.05.009 – volume: 109 start-page: 141 issue: 2 year: 2012 ident: 10.1016/j.biosystems.2014.12.001_bib0080 article-title: The genetic code and its optimization for kinetic energy conservation in polypeptide chains publication-title: Biosystems doi: 10.1016/j.biosystems.2012.03.001 – volume: 363C start-page: 216 year: 2014 ident: 10.1016/j.biosystems.2014.12.001_bib0090 article-title: Species radiation by DNA replication that systematically exchanges nucleotides? publication-title: J. Theor. Biol. doi: 10.1016/j.jtbi.2014.08.036 – volume: 24 start-page: 2096 issue: 18 year: 2008 ident: 10.1016/j.biosystems.2014.12.001_bib0095 article-title: BioJava: an open-source framework for bioinformatics publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn397 – volume: 20 start-page: 641 issue: 5 year: 2013 ident: 10.1016/j.biosystems.2014.12.001_bib0175 article-title: The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome publication-title: Nat. Struct. Mol. Biol. doi: 10.1038/nsmb.2545 – volume: 336 start-page: 221 issue: 0 year: 2013 ident: 10.1016/j.biosystems.2014.12.001_bib0040 article-title: On dichotomic classes and bijections of the genetic code publication-title: J. Theor. Biol. doi: 10.1016/j.jtbi.2013.07.027 – volume: 3 start-page: 37 year: 2008 ident: 10.1016/j.biosystems.2014.12.001_bib0060 article-title: An extension of the coevolution theory of the origin of the genetic code publication-title: Biol. Direct doi: 10.1186/1745-6150-3-37 – volume: 13 start-page: 191 issue: 2 year: 2004 ident: 10.1016/j.biosystems.2014.12.001_bib0075 article-title: Kinetic determinants of high-fidelity tRNA discrimination on the ribosome publication-title: Mol. Cell doi: 10.1016/S1097-2765(04)00005-X – year: 2008 ident: 10.1016/j.biosystems.2014.12.001_bib0070 article-title: The mathematical structure of the genetic code – volume: 43 start-page: 416 issue: 5 year: 1957 ident: 10.1016/j.biosystems.2014.12.001_bib0020 article-title: Codes without commas publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.43.5.416 – volume: 38 start-page: 367 issue: 3 year: 1968 ident: 10.1016/j.biosystems.2014.12.001_bib0025 article-title: The origin of the genetic code publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(68)90392-6 – volume: 182 start-page: 45 issue: 1 year: 1996 ident: 10.1016/j.biosystems.2014.12.001_bib0010 article-title: A complementary circular code in the protein coding genes publication-title: J. Theor. Biol. doi: 10.1006/jtbi.1996.0142 – volume: 461 start-page: 1234 issue: 7268 year: 2009 ident: 10.1016/j.biosystems.2014.12.001_bib0145 article-title: What recent ribosome structures have revealed about the mechanism of translation publication-title: Nature doi: 10.1038/nature08403 – volume: 61 start-page: 99 issue: 2 year: 2009 ident: 10.1016/j.biosystems.2014.12.001_bib0105 article-title: Origin and evolution of the genetic code: the universal enigma publication-title: IUBMB Life doi: 10.1002/iub.146 – volume: 33 start-page: 412 issue: 5 year: 1991 ident: 10.1016/j.biosystems.2014.12.001_bib0085 article-title: A quantitative measure of error minimization in the genetic code publication-title: J. Mol. Evol. doi: 10.1007/BF02103132 – volume: 111 start-page: 721 issue: 5 year: 2002 ident: 10.1016/j.biosystems.2014.12.001_bib0130 article-title: Selection of tRNA by the ribosome requires a transition from an open to a closed form publication-title: Cell doi: 10.1016/S0092-8674(02)01086-3 – volume: 249 start-page: 162 issue: 1 year: 2007 ident: 10.1016/j.biosystems.2014.12.001_bib0150 article-title: Cost minimization of ribosomal frameshifts publication-title: J. Theor. Biol. doi: 10.1016/j.jtbi.2007.07.007 – volume: 484 start-page: 256 issue: 7393 year: 2012 ident: 10.1016/j.biosystems.2014.12.001_bib0030 article-title: A new understanding of the decoding principle on the ribosome publication-title: Nature doi: 10.1038/nature10913 – volume: 33 start-page: 457 issue: 4-5 year: 2003 ident: 10.1016/j.biosystems.2014.12.001_bib0045 article-title: The case for an error minimizing standard genetic code publication-title: Orig. Life Evol. Biosph. doi: 10.1023/A:1025771327614 – volume: 78 start-page: 051918 issue: 5 Pt 1 year: 2008 ident: 10.1016/j.biosystems.2014.12.001_bib0065 article-title: Strong short-range correlations and dichotomic codon classes in coding DNA sequences publication-title: Phys. Rev. E: Stat. Nonlin. Soft Matter Phys. doi: 10.1103/PhysRevE.78.051918 – volume: 292 start-page: 897 issue: 5518 year: 2001 ident: 10.1016/j.biosystems.2014.12.001_bib0125 article-title: Recognition of cognate transfer RNA by the 30s ribosomal subunit publication-title: Science doi: 10.1126/science.1060612 – volume: 125C start-page: 22 year: 2014 ident: 10.1016/j.biosystems.2014.12.001_bib0155 article-title: Mitochondrial swinger replication: DNA replication systematically exchanging nucleotides and short 16s ribosomal DNA swinger inserts publication-title: Biosystems doi: 10.1016/j.biosystems.2014.09.012 – volume: 106 start-page: 489 issue: 3 year: 1993 ident: 10.1016/j.biosystems.2014.12.001_bib0100 article-title: Evolutionary changes in the genetic code publication-title: Comp. Biochem. Physiol. B doi: 10.1016/0305-0491(93)90122-L – volume: 73 start-page: 178 issue: 1 year: 2009 ident: 10.1016/j.biosystems.2014.12.001_bib0015 article-title: A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight p-site realignment publication-title: Microbiol. Mol. Biol. Rev. doi: 10.1128/MMBR.00010-08 – volume: 70 start-page: 1875 issue: 11 year: 2013 ident: 10.1016/j.biosystems.2014.12.001_bib0110 article-title: RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence publication-title: Cell. Mol. Life Sci. – volume: 56 start-page: 229 issue: 1 year: 1992 ident: 10.1016/j.biosystems.2014.12.001_bib0135 article-title: Recent evidence for evolution of the genetic code publication-title: Microbiol. Rev. doi: 10.1128/MMBR.56.1.229-264.1992 – volume: 37 start-page: 24 year: 2012 ident: 10.1016/j.biosystems.2014.12.001_bib0115 article-title: Circular code motifs in transfer and 16s ribosomal RNAs: a possible translation code in genes publication-title: Comput. Biol. Chem. doi: 10.1016/j.compbiolchem.2011.10.002 – year: 2010 ident: 10.1016/j.biosystems.2014.12.001_bib0120 – volume: 366 start-page: 1 issue: 1 year: 2007 ident: 10.1016/j.biosystems.2014.12.001_bib0005 article-title: tRNA's wobble decoding of the genome: 40 years of modification publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2006.11.046 – volume: 370 start-page: 2987 issue: 1969 year: 2012 ident: 10.1016/j.biosystems.2014.12.001_bib0055 article-title: DNA, dichotomic classes and frame synchronization: a quasi-crystal framework publication-title: Philos. Trans. A: Math. Phys. Eng. Sci. doi: 10.1098/rsta.2011.0387 – volume: 16 start-page: 141 issue: 1 year: 2010 ident: 10.1016/j.biosystems.2014.12.001_bib0165 article-title: Revisiting the operational RNA code for amino acids: ensemble attributes and their implications publication-title: RNA doi: 10.1261/rna.1745910 – volume: 72 start-page: 1909 issue: 5 year: 1975 ident: 10.1016/j.biosystems.2014.12.001_bib0180 article-title: A co-evolution theory of the genetic code publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.72.5.1909 – volume: 173 start-page: 318 year: 1954 ident: 10.1016/j.biosystems.2014.12.001_bib0050 article-title: Possible relation between deoxyribonucleic acid and protein structures publication-title: Nature doi: 10.1038/173318a0 – volume: 63 start-page: 297 issue: 3 year: 2006 ident: 10.1016/j.biosystems.2014.12.001_bib0160 article-title: The coevolution of genes and genetic codes: Crick's frozen accident revisited publication-title: J. Mol. Evol. doi: 10.1007/s00239-004-0176-7 – volume: 52 start-page: 9 year: 2014 ident: 10.1016/j.biosystems.2014.12.001_bib0170 article-title: Circular code motifs in the ribosome decoding center publication-title: Comput. Biol. Chem. doi: 10.1016/j.compbiolchem.2014.08.001 – volume: 167 start-page: 1393 issue: 6 year: 1966 ident: 10.1016/j.biosystems.2014.12.001_bib0140 article-title: Codon systematization in the genetic code publication-title: Dokl. Akad. Nauk. SSSR |
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| SubjectTerms | Algorithms Computational Biology - methods Dichotomic partition Genetic code Genetic Code - genetics Models, Genetic Ribosome Rumer Scan algorithm Software |
| Title | On models of the genetic code generated by binary dichotomic algorithms |
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