Viral Metagenomics: MetaView Software

Zhou, C ; Smith, J

关键词: DESIGN;    NUCLEIC ACIDS;    BIOLOGY;   

DOI  :  10.2172/923102
RP-ID  :  UCRL-TR-236531
PID  :  OSTI ID: 923102
Others  :  TRN: US200806%%362

学科分类：生物科学（综合）

美国|英语

来源: SciTech Connect

【 摘 要 】

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.