Publication detail

Automated Detection of Endogenous Viral Elements in Host Genomes

BUCHMAN, J. ZILE, K. GLICKMAN, C. KUPKOVÁ, K. WALDMAN, J. ELLISON, M. CANTALUPO, P. BUSBY, B.

Original Title

Automated Detection of Endogenous Viral Elements in Host Genomes

Type

abstract

Language

English

Original Abstract

Endogenous Viral Elements (EVEs) are part of the host genome and allow horizontal transmission within a host, but the underlying evolutionary mechanisms are still unclear. Metagenomic sequencing data sets contain a wealth of information, including sequences from viruses. Such datasets present an opportunity to analyze known EVEs and discover new ones. We introduce a new method for extending viral contiguous sequences or contigs through the Building Up Domains (BUD) algorithm (https://github.com/NCBI-Hackathons/ViruSpy) that identifies virus DNA from sequencing experiments. This methodology differs from current virus discovery tools by iteratively building upon sequences that are known to contain a viral protein domains, and searching for surrounding non-viral protein domains. We designed EndoVir (https://github.com/NCBI-Hackathons/endovir) to implement BUD in Python3. To reduce the use of temporary files, data is streamed between processes where possible, e.g. we use MagicBLAST to screen the metagenomic datasets as it can read NCBI’s SRA format directly. Our implementation analyzes the results from each individual pipeline step and allows real-time parameter adjustment. This approach allows us to adjust for the diversity present in metagenomic data sets.

Keywords

ViruSpy, Metagenome, Virus

Authors

BUCHMAN, J.; ZILE, K.; GLICKMAN, C.; KUPKOVÁ, K.; WALDMAN, J.; ELLISON, M.; CANTALUPO, P.; BUSBY, B.

Released

17. 1. 2018

Location

San Diego, CA

Pages from

1

Pages to

1

Pages count

1

URL

https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31074

BibTex

@misc{BUT144370,
  author="Jan P {Buchman} and Karina {Zile} and Cody {Glickman} and Kristýna {Kupková} and Jacob {Waldman} and Mitch {Ellison} and Paul {Cantalupo} and Ben {Busby}",
  title="Automated Detection of Endogenous Viral Elements in Host Genomes",
  year="2018",
  pages="1--1",
  address="San Diego, CA",
  url="https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31074",
  note="abstract"
}