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Methods Mol Biol. 2018;1838:261-272. doi: 10.1007/978-1-4939-8682-8_18.

Bioinformatics Assembling and Assessment of Novel Coxsackievirus B1 Genome.

Author information

1
Computational Biology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland. jakelin@uta.fi.
2
Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland. jakelin@uta.fi.
3
Computational Biology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.
4
Virology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.

Abstract

The human microbiome project via application of metagenomic next-generation sequencing techniques has found surprising large and diverse amounts of microbial sequences across different body sites. There is a wave of investigators studying autoimmune related diseases designing from birth case and control studies to elucidate microbial associations and potential direct triggers. Sequencing analysis, considered big data as it typically includes millions of reads, is challenging but particularly demanding and complex is virome profiling due to its lack of pan-viral genomic signature. Impressively thousands of virus complete genomes have been deposited and these high-quality references are core components of virus profiling pipelines and databases. Still it is commonly known that most viral sequences do not map to known viruses. Moreover human viruses, particularly RNA groups, are notoriously heterogeneous due to high mutation rates. Here, we present the related assembling challenges and a series of bioinformatics steps that were applied in the construction of the complete consensus genome of a novel clinical isolate of Coxsackievirus B1. We further demonstrate our effort in calling mutations between prototype Coxsackievirus B1 sequence from GenBank and serial clinical isolate genome grown in cell culture.

KEYWORDS:

Assembly; Bioinformatics; Coxsackievirus; Enterovirus; Genomics; T1D

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