ArticleProceedings of the National Academy of Sciences of the United States of America2007
Distinctive features of large complex virus genomes and proteomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
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- CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase.Bioinformatics (Oxford, England) · 2021Article
- A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms.BMC genomics · 2019Article
- Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution.Journal of molecular evolution · 2019Article
- New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.Briefings in bioinformatics · 2014Review
- Finding and identifying the viral needle in the metagenomic haystack: trends and challenges.Frontiers in microbiology · 2014Article
- Analysis of dinucleotide signatures in HIV-1 subtype B genomes.Journal of genetics · 2013Article
- Coevolution between simple sequence repeats (SSRs) and virus genome size.BMC genomics · 2012Article
- Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Abundant oligonucleotides common to most bacteria.PloS one · 2010Article
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- Genomic DNA k-mer spectra: models and modalities.Genome biology · 2009Article
- Non-random pre-transcriptional evolution in HIV-1. A refutation of the foundational conditions for neutral evolution.Genetics and molecular biology · 2009Article
- Community-wide analysis of microbial genome sequence signatures.Genome biology · 2009Article
- Micro- and nanotechnology for viral detection.Analytical and bioanalytical chemistry · 2009Review
- A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.Genome biology · 2009Article
- Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.Nucleic acids research · 2008Article
- The next meta-challenge for Bioinformatics.Bioinformation · 2008Article
- Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses.BMC genomics · 2007Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
More than a dozen large DNA viruses exceeding 240-kb genome size were recently discovered, including the "giant" mimivirus with a 1.2-Mb genome size. The detection of mimivirus and other large viruses has stimulated new analysis and discussion concerning the early evolution of life and the complexity and mechanisms of evolutionary transitions. This paper presents analysis in three contexts. (i) Genome signatures of large viruses tend to deviate from the genome signatures of their hosts, perhaps indicating that the large viruses are lytic in the hosts. (ii) Proteome composition within these viral genomes contrast with cellular organisms; for example, most eukaryotic genomes, with respect to acidic residue usages, select Glu over Asp, but the opposite generally prevails for the large viral genomes preferring Asp more than Glu. In comparing Phe vs. Tyr usage, the viral genomes select mostly Tyr over Phe, whereas in almost all bacterial and eukaryotic genomes, Phe is used more than Tyr. Interpretations of these contrasts are proffered with respect to protein structure and function. (iii) Frequent oligonucleotides and peptides are characterized in the large viral genomes. The frequent words may provide structural flexibility to interact with host proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.