The Phylogenetic Utility of the Codon-Degeneracy Model

2000 ◽  
Vol 51 (3) ◽  
pp. 185-193 ◽  
Author(s):  
David A. McClellan
Keyword(s):  
Codon Degeneracy

scholarly journals Group-specific identification of polioviruses by PCR using primers containing mixed-base or deoxyinosine residue at positions of codon degeneracy.

1996 ◽  
Vol 34 (12) ◽  
pp. 2990-2996 ◽  
Author(s):  
D R Kilpatrick ◽  
B Nottay ◽  
C F Yang ◽  
S J Yang ◽  
M N Mulders ◽  
...  
Keyword(s):  
Specific Identification ◽  
Codon Degeneracy

scholarly journals Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc (N̂c) and ENCprime (N̂′c) measures

2017 ◽  
Vol 22 (3) ◽  
pp. 277-283 ◽  
Author(s):  
Siddhartha Sankar Satapathy ◽  
Ajit Kumar Sahoo ◽  
Suvendra Kumar Ray ◽  
Tapash Chandra Ghosh
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Degeneracy

scholarly journals Serotype-Specific Identification of Polioviruses by PCR Using Primers Containing Mixed-Base or Deoxyinosine Residues at Positions of Codon Degeneracy

1998 ◽  
Vol 36 (2) ◽  
pp. 352-357 ◽  
Author(s):  
David R. Kilpatrick ◽  
Baldev Nottay ◽  
Chen-Fu Yang ◽  
Su-Ju Yang ◽  
Edson Da Silva ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
High Rate ◽  
Rapid Screening ◽  
Reaction Conditions ◽  
Specific Primers ◽  
Specific Identification ◽  
Primer Sets ◽  
Reference Strains ◽  
Codon Degeneracy

We have developed a method for determining the serotypes of poliovirus isolates by PCR. Three sets of serotype-specific antisense PCR-initiating primers (primers seroPV1A, seroPV2A, and seroPV3A) were designed to pair with codons of VP1 amino acid sequences that are conserved within but that differ across serotypes. The sense polarity primers (primers seroPV1S, seroPV2S, and seroPV3S) matched codons of more conserved capsid sequences. The primers contain mixed-base and deoxyinosine residues to compensate for the high rate of degeneracy of the targeted codons. The serotypes of all polioviruses tested (48 vaccine-related isolates and 110 diverse wild isolates) were correctly identified by PCR with the serotype-specific primers. None of the genomic sequences of 49 nonpolio enterovirus reference strains were amplified under equivalent reaction conditions with any of the three primer sets. These primers are useful for the rapid screening of poliovirus isolates and for determining the compositions of cultures containing mixtures of poliovirus serotypes.

A tetrahedral representation of poly-codon sequences and a possible origin of codon degeneracy

1984 ◽  
Vol 108 (3) ◽  
pp. 459-468 ◽  
Author(s):  
L.E.H. Trainor ◽  
G.W. Rowe ◽  
V.L. Szabo
Keyword(s):  
Codon Degeneracy
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