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MG-Digger: An Automated Pipeline to Search for Giant Virus-Related Sequences in Metagenomes

Verneau, Jonathan ; Levasseur, Anthony ; Raoult, Didier ; La Scola, Bernard ; Colson, Philippe; Combe, Isabelle (Editor)

Frontiers in Microbiology, March 2016, Vol.7 [Tạp chí có phản biện]

ISSN: 1664-302X ; E-ISSN: 1664-302X ; DOI: 10.3389/fmicb.2016.00428

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  • Nhan đề:
    MG-Digger: An Automated Pipeline to Search for Giant Virus-Related Sequences in Metagenomes
  • Tác giả: Verneau, Jonathan ; Levasseur, Anthony ; Raoult, Didier ; La Scola, Bernard ; Colson, Philippe
  • Combe, Isabelle (Editor)
  • Chủ đề: Life Sciences ; Human Health and Pathology ; Infectious Diseases ; Mimivirus ; Bioinformatics ; Pipeline ; Metagenomes ; Giant Virus ; Megavirales ; Biology
  • Là 1 phần của: Frontiers in Microbiology, March 2016, Vol.7
  • Mô tả: The number of metagenomic studies conducted each year is growing dramatically. Storage and analysis of such big data is difficult and time-consuming. Interestingly, analysis shows that environmental and human metagenomes include a significant amount of non-annotated sequences, representing a `dark matter.' We established a bioinformatics pipeline that automatically detects metagenome reads matching query sequences from a given set and applied this tool to the detection of sequences matching large and giant DNA viral members of the proposed order Megavirales or virophages. A total of 1,045 environmental and human metagenomes (approximate to Terabase) were collected, processed, and stored on our bioinformatics server. In addition, nucleotide and protein sequences from 93 Megavirales representatives, including 19 giant viruses of amoeba, and 5 virophages, were collected. The pipeline was generated by scripts written in Python language and entitled MG-Digger. Metagenomes previously...
  • Ngôn ngữ: English
  • Số nhận dạng: ISSN: 1664-302X ; E-ISSN: 1664-302X ; DOI: 10.3389/fmicb.2016.00428

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