title: Identification and chronological analysis of genomic signatures in influenza A viruses.
abstract: An increase in the availability of data on the influenza A viruses (IAV) has enabled the identification of the potential determinants of IAV host specificity using computational approaches. In this study, we proposed an alternative approach, based on the adjusted Rand index (ARI), for the evaluation of genomic signatures of IAVs and their ability to distinguish hosts they infected. Our experiments showed that the host-specific signatures identified using the ARI were more characteristic of their hosts than those identified using previous measures. Our results provided updates on the host-specific genomic signatures in the internal proteins of the IAV based on the sequence data as of February 2013 in the National Center for Biotechnology Information (NCBI). Unlike other approaches for signature recognition, our approach considered not only the ability of signatures to distinguish hosts (according to the ARI), but also the chronological relationships among proteins. We identified novel signatures that could be mapped to known functional domains, and introduced a chronological analysis to investigate the changes in host-specific genomic signatures over time. Our chronological analytical approach provided results on the adaptive variability of signatures, which correlated with previous studies' findings, and indicated prospective adaptation trends that warrant further investigation.
authors.affiliation: Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu, Taiwan ; Department of Computer Science, National Chiao Tung University, Hsinchu, Taiwan.
authors.forename: Yuh-Jyh
authors.initials: YJ
authors.lastname: Hu
authors.affiliation: Department of Computer Science, National Chiao Tung University, Hsinchu, Taiwan.
authors.forename: Po-Chin
authors.initials: PC
authors.lastname: Tu
authors.affiliation: Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu, Taiwan.
authors.forename: Chun-Sheng
authors.initials: CS
authors.lastname: Lin
authors.affiliation: Department of Computer Science, National Chiao Tung University, Hsinchu, Taiwan.
authors.forename: Szu-Ting
authors.initials: ST
authors.lastname: Guo
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D016679:Genome, Viral / Q000235:genetics; D023281:Genomics; D058507:Host Specificity; D006801:Humans; D009980:Influenza A virus / Q000235:genetics* / Q000502:physiology; D013997:Time Factors