TY - JOUR
T1 - G-FLUA2H
T2 - A web-based application to study the dynamics of animal-to-human mutation transmission for influenza viruses
AU - Sjaugi, Muhammad Farhan
AU - Tan, Swan
AU - Abd Raman, Hadia Syahirah
AU - Lim, Wan Ching
AU - Nik Mohamed, Nik Elena
AU - August, J. Thomas
AU - Khan, Asif M.
N1 - Funding Information:
Publication costs for this article were funded by Perdana University. This article has been published as part of BMC Medical Genomics Volume 8 Supplement 4, 2015: Joint 26th Genome Informatics Workshop and 14th International Conference on Bioinformatics: Medical genomics. The full contents of the supplement are available online at http://www. biomedcentral.com/bmcmedgenomics/supplements/8/S4.
Publisher Copyright:
© 2015 Sjaugi et al.
PY - 2015/12/9
Y1 - 2015/12/9
N2 - g-FLUA2H is a web-based application focused on the analysis of the dynamics of influenza virus animal-to-human (A2H) mutation transmissions. The application only requires the viral protein sequences from both the animal and human host populations as input datasets. The comparative analyses between the co-aligned sequences of the two viral populations is based on a sliding window approach of size nine for statistical significance and data application to the major histocompatibility complex (MHC) and T-cell receptor (TCR) immune response mechanisms. The sequences at each of the aligned overlapping nonamer positions for the respective virus hosts are classified as four patterns of characteristic diversity motifs, as a basis for quantitative analyses: (i) "index", the most prevalent sequence; (ii) "major" variant, the second most common sequence and the single most prevalent variant of the index, with at least one amino acid mutation; (iii) "minor" variants, multiple different sequences, each with an incidence (percent occurrence) less than that of the major variant; and (iv) "unique" variants, each with only one occurrence in the alignment. The diversity motifs and their incidences at each of the nonamer positions allow evaluation of the mutation transmission dynamics and selectivity of the viral sequences in relation to the animal and the human hosts. g-FLUA2H is facilitated by a grid back-end for parallel processing of large sequence datasets. The web-application is publicly available at http://bioinfo.perdanauniversity.edu.my/g-FLUA2H. It can be used for a detailed characterization of the composition and incidence of mutations present in the proteomes of influenza viruses from animal and human host populations, for a better understanding of host tropism.
AB - g-FLUA2H is a web-based application focused on the analysis of the dynamics of influenza virus animal-to-human (A2H) mutation transmissions. The application only requires the viral protein sequences from both the animal and human host populations as input datasets. The comparative analyses between the co-aligned sequences of the two viral populations is based on a sliding window approach of size nine for statistical significance and data application to the major histocompatibility complex (MHC) and T-cell receptor (TCR) immune response mechanisms. The sequences at each of the aligned overlapping nonamer positions for the respective virus hosts are classified as four patterns of characteristic diversity motifs, as a basis for quantitative analyses: (i) "index", the most prevalent sequence; (ii) "major" variant, the second most common sequence and the single most prevalent variant of the index, with at least one amino acid mutation; (iii) "minor" variants, multiple different sequences, each with an incidence (percent occurrence) less than that of the major variant; and (iv) "unique" variants, each with only one occurrence in the alignment. The diversity motifs and their incidences at each of the nonamer positions allow evaluation of the mutation transmission dynamics and selectivity of the viral sequences in relation to the animal and the human hosts. g-FLUA2H is facilitated by a grid back-end for parallel processing of large sequence datasets. The web-application is publicly available at http://bioinfo.perdanauniversity.edu.my/g-FLUA2H. It can be used for a detailed characterization of the composition and incidence of mutations present in the proteomes of influenza viruses from animal and human host populations, for a better understanding of host tropism.
KW - animal-to-human transmission
KW - influenza viruses
KW - mutation
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U2 - 10.1186/1755-8794-8-S4-S5
DO - 10.1186/1755-8794-8-S4-S5
M3 - Article
C2 - 26680743
AN - SCOPUS:84962433214
SN - 1755-8794
VL - 8
JO - BMC Medical Genomics
JF - BMC Medical Genomics
IS - 4
M1 - 570
ER -