Codon choice in genes depends on flanking sequence information - Implications for theoretical reverse translation

Karthikeyan Sivaraman, Aswinsainarain Seshasayee, Patrick Tarwater, Alexander M. Cole

Research output: Contribution to journalArticle

Abstract

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods NCM and c-NCM, we were able to increase the average sequence identity from 77% up to 81%. Furthermore, we revealed a significant increase in coverage, at 80% identity, from < 20% (CSM) to > 75 (c-NCM). The algorithms, their applications and implications are discussed herein.

Original languageEnglish (US)
Article numbere16
JournalNucleic acids research
Volume36
Issue number3
DOIs
StatePublished - Feb 1 2008
Externally publishedYes

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Codon
Genes
Proteins
Polymerase Chain Reaction
Peptides

ASJC Scopus subject areas

  • Genetics

Cite this

Codon choice in genes depends on flanking sequence information - Implications for theoretical reverse translation. / Sivaraman, Karthikeyan; Seshasayee, Aswinsainarain; Tarwater, Patrick; Cole, Alexander M.

In: Nucleic acids research, Vol. 36, No. 3, e16, 01.02.2008.

Research output: Contribution to journalArticle

Sivaraman, Karthikeyan ; Seshasayee, Aswinsainarain ; Tarwater, Patrick ; Cole, Alexander M. / Codon choice in genes depends on flanking sequence information - Implications for theoretical reverse translation. In: Nucleic acids research. 2008 ; Vol. 36, No. 3.
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