Dataset Information

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

ABSTRACT: Next generation sequencing (NGS) is superseding Sanger technology for analysing intra-host viral populations, in terms of genome length and resolution. We introduce two new empirical validation data sets and test the available viral population assembly software. Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced using Roche's 454 sequencing platform. The performance of different assemblers was compared in terms of phylogenetic clustering and recombination with the Sanger clones. Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent lineages, but none were able to provide a high precision/recall tradeoff. Estimated variant frequencies mildly correlated with the original. Given the limitations of currently available algorithms identified by our empirical validation, the development and exploitation of additional data sets is needed, in order to establish an efficient framework for viral population reconstruction using NGS.

SUBMITTER: Prosperi MC

PROVIDER: S-EPMC3789152 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

Prosperi Mattia C F MC Yin Li L Nolan David J DJ Lowe Amanda D AD Goodenow Maureen M MM Salemi Marco M

Scientific reports 20131003

Next generation sequencing (NGS) is superseding Sanger technology for analysing intra-host viral populations, in terms of genome length and resolution. We introduce two new empirical validation data sets and test the available viral population assembly software. Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced using Roche's 454 sequencing ...[more]

PMID: 24089188

Similar Datasets

Project description:Nanomaterials are commonly considered as those materials in which the shape and molecular composition at a nanometer scale can be controlled. Subsequently, they present extraordinary properties that are being useful for the development of new and improved applications in many fields, including medicine. In dentistry, several research efforts are being conducted, especially during the last decade, for the improvement of the properties of materials used in dentistry. The objective of the present article is to offer the audience a complete and comprehensive review of the main applications that have been developed in dentistry, by the use of these materials, during the last two decades. It was shown how these materials are improving the treatments in mainly all the important areas of dentistry, such as endodontics, periodontics, implants, tissue engineering and restorative dentistry. The scope of the present review is, subsequently, to revise the main applications regarding nano-shaped materials in dentistry, including nanorods, nanofibers, nanotubes, nanospheres/nanoparticles, and zeolites and other orders porous materials. The results of the bibliographic analysis show that the most explored nanomaterials in dentistry are graphene and carbon nanotubes, and their derivatives. A detailed analysis and a comparative study of their applications show that, although they are quite similar, graphene-based materials seem to be more promising for most of the applications of interest in dentistry. The bibliographic study also demonstrated the potential of zeolite-based materials, although the low number of studies on their applications shows that they have not been totally explored, as well as other porous nanomaterials that have found important applications in medicine, such as metal organic frameworks, have not been explored. Subsequently, it is expected that the research effort will concentrate on graphene and zeolite-based materials in the coming years. Thus, the present review paper presents a detailed bibliographic study, with more than 200 references, in order to briefly describe the main achievements that have been described in dentistry using nanomaterials, compare and analyze them in a critical way, with the aim of predicting the future challenges.

Dataset Information

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

Publications

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets