Circular Codes in the Genetic Information
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© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
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Codes are the sets of words over arbitrary alphabets with the property of unique
decipherability.
Circular codes are a special class of codes. They are the sets of words with the property
of unique recognition of the reading frame for any sequence composed of them and
written on a circle. They were introduced by Golomb and Gordon in the 60s under the
name of codes with bounded synchronization delay, because they have a strong property
of synchronization. For this reason, they play an important role in problems of error
correction.
In the middle 90’s such a circular code X was identified in the genes of bacteria, eukaryotes,
plasmids, and viruses by a comprehensive statistical investigation. The code X contained
the 20 trinucleotides that appeared to be the codons that had the highest preference for
the correct reading frame compared to frames 1 and 2. Since then intensive research
on circular codes in the genetic information and their potential role in maintaining the
corr...ect reading frame during the translation process in the ribosome has been done by
various authors. In particular, X-motifs were identified in (i) genes “universally” (ii) tRNAs
of prokaryotes and eukaryotes; (iii) rRNAs of prokaryotes (16S) and eukaryotes (18S), in
particular in the ribosome decoding center where the universally conserved nucleotides
G530, A1492, and A1493 are included in the X-motif; and (iv) genomes (non-coding
regions of eukaryotes). Circular codes have a highly complex structure and the ones found
in genes possess additional properties like e.g. self-complementarity that reflect their
biological nature.
In our talk we give a short introduction to the theory of circular codes and an overview on
the methods from mathematics, statistics and bioinformatics to explore their properties
and their biological role. Finally, a possible model of the evolution of the genetic code from
the perspective of circular code theory is presented.
Keywords:
circular codes / genetic code / frame-shift / translationSource:
4th Belgrade Bioinformatics Conference, 2023, 4, 21-21Publisher:
- Belgrade : Institute of molecular genetics and genetic engineering
Note:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
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Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Fimmel, Elena AU - Strüngmann, Lutz PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1957 AB - Codes are the sets of words over arbitrary alphabets with the property of unique decipherability. Circular codes are a special class of codes. They are the sets of words with the property of unique recognition of the reading frame for any sequence composed of them and written on a circle. They were introduced by Golomb and Gordon in the 60s under the name of codes with bounded synchronization delay, because they have a strong property of synchronization. For this reason, they play an important role in problems of error correction. In the middle 90’s such a circular code X was identified in the genes of bacteria, eukaryotes, plasmids, and viruses by a comprehensive statistical investigation. The code X contained the 20 trinucleotides that appeared to be the codons that had the highest preference for the correct reading frame compared to frames 1 and 2. Since then intensive research on circular codes in the genetic information and their potential role in maintaining the correct reading frame during the translation process in the ribosome has been done by various authors. In particular, X-motifs were identified in (i) genes “universally” (ii) tRNAs of prokaryotes and eukaryotes; (iii) rRNAs of prokaryotes (16S) and eukaryotes (18S), in particular in the ribosome decoding center where the universally conserved nucleotides G530, A1492, and A1493 are included in the X-motif; and (iv) genomes (non-coding regions of eukaryotes). Circular codes have a highly complex structure and the ones found in genes possess additional properties like e.g. self-complementarity that reflect their biological nature. In our talk we give a short introduction to the theory of circular codes and an overview on the methods from mathematics, statistics and bioinformatics to explore their properties and their biological role. Finally, a possible model of the evolution of the genetic code from the perspective of circular code theory is presented. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Circular Codes in the Genetic Information EP - 21 SP - 21 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_1957 ER -
@conference{ author = "Fimmel, Elena and Strüngmann, Lutz", year = "2023", abstract = "Codes are the sets of words over arbitrary alphabets with the property of unique decipherability. Circular codes are a special class of codes. They are the sets of words with the property of unique recognition of the reading frame for any sequence composed of them and written on a circle. They were introduced by Golomb and Gordon in the 60s under the name of codes with bounded synchronization delay, because they have a strong property of synchronization. For this reason, they play an important role in problems of error correction. In the middle 90’s such a circular code X was identified in the genes of bacteria, eukaryotes, plasmids, and viruses by a comprehensive statistical investigation. The code X contained the 20 trinucleotides that appeared to be the codons that had the highest preference for the correct reading frame compared to frames 1 and 2. Since then intensive research on circular codes in the genetic information and their potential role in maintaining the correct reading frame during the translation process in the ribosome has been done by various authors. In particular, X-motifs were identified in (i) genes “universally” (ii) tRNAs of prokaryotes and eukaryotes; (iii) rRNAs of prokaryotes (16S) and eukaryotes (18S), in particular in the ribosome decoding center where the universally conserved nucleotides G530, A1492, and A1493 are included in the X-motif; and (iv) genomes (non-coding regions of eukaryotes). Circular codes have a highly complex structure and the ones found in genes possess additional properties like e.g. self-complementarity that reflect their biological nature. In our talk we give a short introduction to the theory of circular codes and an overview on the methods from mathematics, statistics and bioinformatics to explore their properties and their biological role. Finally, a possible model of the evolution of the genetic code from the perspective of circular code theory is presented.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Circular Codes in the Genetic Information", pages = "21-21", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_1957" }
Fimmel, E.,& Strüngmann, L.. (2023). Circular Codes in the Genetic Information. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 21-21. https://hdl.handle.net/21.15107/rcub_imagine_1957
Fimmel E, Strüngmann L. Circular Codes in the Genetic Information. in 4th Belgrade Bioinformatics Conference. 2023;4:21-21. https://hdl.handle.net/21.15107/rcub_imagine_1957 .
Fimmel, Elena, Strüngmann, Lutz, "Circular Codes in the Genetic Information" in 4th Belgrade Bioinformatics Conference, 4 (2023):21-21, https://hdl.handle.net/21.15107/rcub_imagine_1957 .