arXiv (Cornell University) · 2005 · 34 citations · 32 references
Life SciencesMicrobiologyMolecular BiologyGenomicsMolecular VirologyVirologyDna Virus BiologyViral ClassificationViral Genome OrganizationVirus ClassificationVirus Genome OrganizationVirus TaxonomyAminoacyl-transfer Rna SynthetasesAminoacyl-trna SynthetasesComplexityDouble-stranded Dna VirusesMicrobial BiodiversityTranslation Machinery GenesVirus Genome-based TaxonomyVirus Morphology-based Taxonomy
The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (>400 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified new types of genes not expected to be seen in a virus, such as aminoacyl-tRNA synthetases and other central components of the translation machinery. In this article, we examine how the finding of a giant virus for the first time overlapping with the world of cellular organisms in terms of size and genome complexity might durably influence the way we look at microbial biodiversity, and force us to fundamentally revise our classification of life forms. We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which make them closer to small parasitic prokaryotes than to regular viruses.
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MEGA2: molecular evolutionary genetics analysis software
Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen et al. · Bioinformatics · 2001 · 6.1K citations · Full text
Environmental Genome Shotgun Sequencing of the Sargasso Sea
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Protein homology detection by HMM–HMM comparison
Johannes Söding · Bioinformatics · 2004 · 2.5K citations · Full text
Life Sciences, Bioinformatics, Protein Structure Prediction +16
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