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Title: Viral Metagenomics: MetaView Software

Abstract

The purpose of this report is to design and develop a tool for analysis of raw sequence read data from viral metagenomics experiments. The tool should compare read sequences of known viral nucleic acid sequence data and enable a user to attempt to determine, with some degree of confidence, what virus groups may be present in the sample. This project was conducted in two phases. In phase 1 we surveyed the literature and examined existing metagenomics tools to educate ourselves and to more precisely define the problem of analyzing raw read data from viral metagenomic experiments. In phase 2 we devised an approach and built a prototype code and database. This code takes viral metagenomic read data in fasta format as input and accesses all complete viral genomes from Kpath for sequence comparison. The system executes at the UNIX command line, producing output that is stored in an Oracle relational database. We provide here a description of the approach we came up with for handling un-assembled, short read data sets from viral metagenomics experiments. We include a discussion of the current MetaView code capabilities and additional functionality that we believe should be added, should additional funding be acquired to continuemore » the work.« less

Authors:
;
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
923102
Report Number(s):
UCRL-TR-236531
TRN: US200806%%362
DOE Contract Number:  
W-7405-ENG-48
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DESIGN; NUCLEIC ACIDS; BIOLOGY

Citation Formats

Zhou, C, and Smith, J. Viral Metagenomics: MetaView Software. United States: N. p., 2007. Web. doi:10.2172/923102.
Zhou, C, & Smith, J. Viral Metagenomics: MetaView Software. United States. doi:10.2172/923102.
Zhou, C, and Smith, J. Mon . "Viral Metagenomics: MetaView Software". United States. doi:10.2172/923102. https://www.osti.gov/servlets/purl/923102.
@article{osti_923102,
title = {Viral Metagenomics: MetaView Software},
author = {Zhou, C and Smith, J},
abstractNote = {The purpose of this report is to design and develop a tool for analysis of raw sequence read data from viral metagenomics experiments. The tool should compare read sequences of known viral nucleic acid sequence data and enable a user to attempt to determine, with some degree of confidence, what virus groups may be present in the sample. This project was conducted in two phases. In phase 1 we surveyed the literature and examined existing metagenomics tools to educate ourselves and to more precisely define the problem of analyzing raw read data from viral metagenomic experiments. In phase 2 we devised an approach and built a prototype code and database. This code takes viral metagenomic read data in fasta format as input and accesses all complete viral genomes from Kpath for sequence comparison. The system executes at the UNIX command line, producing output that is stored in an Oracle relational database. We provide here a description of the approach we came up with for handling un-assembled, short read data sets from viral metagenomics experiments. We include a discussion of the current MetaView code capabilities and additional functionality that we believe should be added, should additional funding be acquired to continue the work.},
doi = {10.2172/923102},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Oct 22 00:00:00 EDT 2007},
month = {Mon Oct 22 00:00:00 EDT 2007}
}

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