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Gene. 2013 Jul 10. pii: S0378-1119(13)00828-7. doi: 10.1016/j.gene.2013.06.060. [Epub ahead of print]
Triplet Entropy Analysis of Hemagglutinin and Neuraminidase Sequences Measures Influenza Virus Phylodynamics.
Gerhardt GJ, Takeda AA, Andrighetti T, Sartor IT, Echeverrigaray SL, de Avila E Silva S, Dos Santos L, Rybarczyk-Filho JL.
Source
Departamento de F?sica e Qu?mica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas, 1130 95001-970 - Caxias do Sul, RS - Brasil. Electronic address: gunther_lew@yahoo.com.br.
Abstract
The influenza virus has been a challenge to science due to its ability to withstand new environmental conditions. Taking into account the development of virus sequence databases, computational approaches can be helpful to understand virus behavior along time. Furthermore, they can suggest new directions to deal with influenza. This work presents triplet entropy analysis as a potential phylodynamic tool to quantify nucleotide organization of viral sequences. The application of this measure to segments of Hemagglutinin (HA) and Neuraminidase (NA) of H1N1 and H3N2 virus subtypes has shown some variability effects along timeline, inferring about virus evolution. Sequences were divided by year and compared for virus subtype (H1N1 and H3N2). The nonparametric Mann-Whitney test was used for comparison between groups. Results show that differentiation in entropy precedes differentiation in GC content for both groups. Considering the HA fragment, both triplet entropy as well as GC concentration show intersection in 2009, year of the recent pandemic. Some conclusions about flu possible evolutionary lines were drawn.
? 2013 Elsevier B.V. All rights reserved.
KEYWORDS:
AT, Adenine and Thymine, C-phosphate-G-, CpG, Entropy, GC, Guanine and Cytosine fraction, H1N1, HA, Hemagglutinin, Influenza, NA, Neuraminidase, Power of hydrogen, RNA, Ribonucleic Acid, Sequence analysis, pH
PMID:
23850726
[PubMed - as supplied by publisher]
Triplet Entropy Analysis of Hemagglutinin and Neuraminidase Sequences Measures Influenza Virus Phylodynamics.
Gerhardt GJ, Takeda AA, Andrighetti T, Sartor IT, Echeverrigaray SL, de Avila E Silva S, Dos Santos L, Rybarczyk-Filho JL.
Source
Departamento de F?sica e Qu?mica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas, 1130 95001-970 - Caxias do Sul, RS - Brasil. Electronic address: gunther_lew@yahoo.com.br.
Abstract
The influenza virus has been a challenge to science due to its ability to withstand new environmental conditions. Taking into account the development of virus sequence databases, computational approaches can be helpful to understand virus behavior along time. Furthermore, they can suggest new directions to deal with influenza. This work presents triplet entropy analysis as a potential phylodynamic tool to quantify nucleotide organization of viral sequences. The application of this measure to segments of Hemagglutinin (HA) and Neuraminidase (NA) of H1N1 and H3N2 virus subtypes has shown some variability effects along timeline, inferring about virus evolution. Sequences were divided by year and compared for virus subtype (H1N1 and H3N2). The nonparametric Mann-Whitney test was used for comparison between groups. Results show that differentiation in entropy precedes differentiation in GC content for both groups. Considering the HA fragment, both triplet entropy as well as GC concentration show intersection in 2009, year of the recent pandemic. Some conclusions about flu possible evolutionary lines were drawn.
? 2013 Elsevier B.V. All rights reserved.
KEYWORDS:
AT, Adenine and Thymine, C-phosphate-G-, CpG, Entropy, GC, Guanine and Cytosine fraction, H1N1, HA, Hemagglutinin, Influenza, NA, Neuraminidase, Power of hydrogen, RNA, Ribonucleic Acid, Sequence analysis, pH
PMID:
23850726
[PubMed - as supplied by publisher]
