Home Acta Virologica 2005 Acta Virologica Vol.49, p.169-176, 2005

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Quarterly, 72-88 pp. per issue
Founded: 1957
ISSN 0001-723X
E-ISSN 1336-2305

Published in English

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Acta Virologica Vol.49, p.169-176, 2005

Title: CODON UTILIZATION, DNA LANDSCAPING AND FRACTAL ANALYSIS IN BACTERIOPHAGE Φadh
Author: N.R. McEWAN

Abstract: The bacteriophage Φadh has a low G+C content and encodes its protein products using a restricted number of the codons, which it could theoretically use. Investigated were (i) the restricted codon usage by determining codon indices and codon distances for various genes and ORFs, (ii) distribution of purines and pyrimidines on the two strands of the double-stranded genome and within all genes and ORFs, and (iii) nucleotide positional bias within the genome. The genes and ORFs can be clustered into four groups, based on codon distance analysis. The genome landscape showed that the plus strand was more purine-rich than the negative one and that the only area of the genome where the landscape was located in the pyrimidinerich region was at the start of the sequence which was also the only region of the genome where ORFs were found on the negative strand. The nucleotide composition of the genome, examined by fractal analysis showed little, if any, DNA positional bias, as opposed to overall compositional bias with a self-similarity profile. The ORFs showed a bias in favour of purines on the coding strand.

Keywords: bacteriophage Φadh; codon usage; DNA landscape; fractal analysis
Year: 2005, Volume: 49, Issue: Page From: 169, Page To: 176



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