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J Microbiol Biotechnol. 2016 Jul 27. doi: 10.4014/jmb.1605.05016. [Epub ahead of print]
Insights into the usage of nucleobase triplets and codon context pattern in five influenza A virus subtypes.
Deka H1, Chakraborty S1.
Author information
Abstract
Influenza A virus is a single-stranded RNA virus with a genome of negative polarity. Owing to the antigenic diversity and cross concrete shift, astronomically an immense number of novel strains have developed over the years. The present work deals with the codon utilization partialness among five different influenza A virus isolated from human hosts. All the subtypes showed the homogeneous pattern of nucleotide utilization with a little variation in their utilization frequencies. A lower bias in codon utilization was observed in all the subtypes as reflected by higher magnitudes of an efficacious number of codons. Dinucleotide analysis shows very low CpG utilization and a high predilection of A/T-ending codons. The H5N1 subtype showed noticeable deviation from the rest. Codon pair context analysis showed remarkable depletion of NNC-GNN and NNT-ANN contexts. The findings alluded towards GC-compositional partialness playing a vital role which is reflected in the consequential positive correlation between GC content at different codon positions. Untangling the codon utilization profile would significantly contribute to identify novel drug targets which will pacify the search for antivirals against this virus.
KEYWORDS:
Codon usage bias; codon pair context; dinucleotide; influenza A virus; preferred codon
PMID: 27470283 DOI: 10.4014/jmb.1605.05016
[PubMed - as supplied by publisher]
Insights into the usage of nucleobase triplets and codon context pattern in five influenza A virus subtypes.
Deka H1, Chakraborty S1.
Author information
Abstract
Influenza A virus is a single-stranded RNA virus with a genome of negative polarity. Owing to the antigenic diversity and cross concrete shift, astronomically an immense number of novel strains have developed over the years. The present work deals with the codon utilization partialness among five different influenza A virus isolated from human hosts. All the subtypes showed the homogeneous pattern of nucleotide utilization with a little variation in their utilization frequencies. A lower bias in codon utilization was observed in all the subtypes as reflected by higher magnitudes of an efficacious number of codons. Dinucleotide analysis shows very low CpG utilization and a high predilection of A/T-ending codons. The H5N1 subtype showed noticeable deviation from the rest. Codon pair context analysis showed remarkable depletion of NNC-GNN and NNT-ANN contexts. The findings alluded towards GC-compositional partialness playing a vital role which is reflected in the consequential positive correlation between GC content at different codon positions. Untangling the codon utilization profile would significantly contribute to identify novel drug targets which will pacify the search for antivirals against this virus.
KEYWORDS:
Codon usage bias; codon pair context; dinucleotide; influenza A virus; preferred codon
PMID: 27470283 DOI: 10.4014/jmb.1605.05016
[PubMed - as supplied by publisher]