Assessing Species Diversity Using Metavirome Data: Methods and Challenges
AuthorHerath, D; Jayasundara, D; Ackland, D; Saeed, I; Tang, S-L; Halgamuge, S
Source TitleCOMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
PublisherELSEVIER SCIENCE BV
University of Melbourne Author/sHalgamuge, Saman; Ackland, David; SAEED, ISAAM; Herath Mudiyanselage, Damayanthi
Document TypeJournal Article
CitationsHerath, D; Jayasundara, D; Ackland, D; Saeed, I; Tang, S-L; Halgamuge, S, Assessing Species Diversity Using Metavirome Data: Methods and Challenges, COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2017, 15 pp. 447 - 455
Access StatusOpen Access
Open Access at PMChttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC5650650
ARC Grant codeARC/LP140100670
Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.
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