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Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases
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We compared nucleotide usage pattern conservation for related prokaryotes by examining the representation of DNA tetranucleotide combinations in 27 representative microbial genomes. For each of the organisms studied, tetranucleotide usage departures from expectations (TUD) were shared between related organisms using both Markov chain analysis and a zero-order Markov method. Individual strains, multiple chromosomes, plasmids, and bacteriophages share TUDs within a species. TUDs varied between coding and noncoding DNA. Grouping prokaryotes based on TUD profiles resulted in relationships with important differences from those based on 16S rRNA phylogenies, which may reflect unequal rates of evolution of nucleotide usage patterns following divergence of particular organisms from a common ancestor. By both symmetrical tree distance and likelihood analysis, phylogenetic trees based on TUD profiles demonstrate a level of congruence with 16S rRNA trees similar to that of both RpoA and RecA trees. Congruence of these trees indicates that there exists phylogenetic signal in TUD patterns, most prominent in coding region DNA. Because relationships demonstrated in TUD-based analyses utilize whole genomes, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA.
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“we calculated tetranucleotide usage deviations (TUDs), a strong indicator metric of phylogenetic relatedness (78).”
From Sequence modeling and design from molecular to genome scale with Evo (2024) · cites this paper as [78]
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Cites
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
Tree View: An application to display phylogenetic trees on personal computers
Page, R. (1996) · Computer applications in the biosciences · doi:10.1093/bioinformatics/12.4.357 · Cited by 10,223
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
Woese, C. R., & Fox, G. E. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.11.5088 · Cited by 4,131
The complete genome sequence of the gastric pathogen Helicobacter pylori
Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., et al. (1997) · Nature · doi:10.1038/41483 · Cited by 3,529
A Molecular View of Microbial Diversity and the Biosphere
Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,797
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
Perna, N. T., Plunkett, G., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., et al. (2001) · Nature · doi:10.1038/35054089 · Cited by 2,035
The RDP (Ribosomal Database Project)
Maidak, B. L., Olsen, G. J., Larsen, N. E., Overbeek, R., McCaughey, M. J., & Woese, C. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.109 · Cited by 2,018
The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences
Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C. M., Basham, D., Chillingworth, T., Davies, R. M., Feltwell, T., Holroyd, S. A., et al. (2000) · Nature · doi:10.1038/35001088 · Cited by 1,966
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888
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Items 101–200 of 308
Dalevi, D., Dubhashi, D., & Hermansson, M. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btk029 · Cited by 28
Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies
Wang, Y., Liu, L., Chen, L., Chen, T., & Sun, F. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084348 · Cited by 27
An investigation into inter- and intragenomic variations of graphic genomic signatures
Karamichalis, R., Lila Kari, A., Konstantinidis, S., & Kopecki, S. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0655-4 · Cited by 27
Zhou, Y., Bu, L., Guo, M. A., Zhou, C., Wang, Y., Chen, L., & Liu, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0070241 · Cited by 26
Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake
Bhattarai, B., Bhattacharjee, A. S., Coutinho, F. H., & Goel, R. K. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.701414 · Cited by 26
A simple model to explain three‐base periodicity in coding DNA
Sánchez, J., & López-Villaseñor, I. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.10.056 · Cited by 26
Alignment-Free Genome Tree Inference by Learning Group-Specific Distance Metrics
Patil, K. R., & McHardy, A. C. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt105 · Cited by 24
A novel phage from periodontal pockets associated with chronic periodontitis
Zhang, Y., Shan, T., Li, F. R., Tian, Y., Chen, X., Deng, X., Delwart, E., & Feng, X. (2019) · Virus Genes · doi:10.1007/s11262-019-01658-y · Cited by 25
Patané, J. S. L., Martins, J., & Setúbal, J. C. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7463-4_5 · Cited by 30
GENSTYLE: exploration and analysis of DNA sequences with genomic signature
Fertil, B., Massin, M., Lespinats, S., Devic, C., Dumée, P., & Giron, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki489 · Cited by 25
Zhou, Y., Zhang, W., Wu, H., Huang, K., & Jin, J. (2019) · BMC Genomics · doi:10.1186/s12864-019-6119-x · Cited by 24
Mu, A., Kwong, J. C., Isles, N. S., da Silva, A. G., Schultz, M. B., Ballard, S. A., Lane, C. R., Carter, G. P., Williamson, D. A., Seemann, T., et al. (2019) · mSphere · doi:10.1128/msphere.00529-18 · Cited by 23
Wu, Z., Wang, Y., Zeng, J., & Zhou, Y. (2022) · BMC Genomics · doi:10.1186/s12864-022-08967-x · Cited by 23
Saeed, I., & Halgamuge, S. K. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-s3-s10 · Cited by 22
Bohlin, J., Skjerve, E., & Ussery, D. W. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-487 · Cited by 22
Deaton, J., Yu, F. B., & Quake, S. R. (2019) · Advanced Biosystems · doi:10.1002/adbi.201900108 · Cited by 21
Integrative meta-omics in Galaxy and beyond
Schiml, V. C., Delogu, F., Kumar, P., Kunath, B. J., Batut, B., Mehta, S., Johnson, J. E., Grüning, B. A., Pope, P. B., Jagtap, P. D., et al. (2023) · Environmental Microbiome · doi:10.1186/s40793-023-00514-9 · Cited by 24
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McCarthy, C. G. P., & Fitzpatrick, D. A. (2017) · Advances in genetics · doi:10.1016/bs.adgen.2017.09.006 · Cited by 22
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Gupta, A., & Sharma, V. K. (2015) · BMC Genomics · doi:10.1186/s12864-015-1542-0 · Cited by 19
Li, P., Xie, B., Zhang, X., Qin, Q., Dang, H., Wang, X., Chen, X., Yu, J. M., & Zhang, Y. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02637.x · Cited by 19
Firrao, G., Martini, M., Ermacora, P., Loi, N., Torelli, E., Foissac, X., Carle, P., Kirkpatrick, B. C., Liefting, L. W., Schneider, B., et al. (2013) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2013.07.003 · Cited by 19
Röllinghoff, M., Zarghooni, K., Dargel, J., Schlegel, U. J., Siewe, J., Eysel, P., & Sobottke, R. (2010) · PubMed · Cited by 19
Next generation sequencing reads comparison with an alignment-free distance
Weitschek, E., Santoni, D., Fiscon, G., Cola, M. C. D., Bertolazzi, P., & Felici, G. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-869 · Cited by 18
AMP 0 : Species-Specific Prediction of Anti-microbial Peptides Using Zero and Few Shot Learning
Gull, S., & Minhas, F. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.2999399 · Cited by 26
Dziuba, M. V., Paulus, A., Schramm, L., Awal, R. P., Pósfai, M., Monteil, C. L., Fouteau, S., Uebe, R., & Schüler, D. (2022) · The ISME Journal · doi:10.1038/s41396-022-01348-y · Cited by 18
Teeling, H., & Glöckner, F. O. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-66 · Cited by 18
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Kang, D., Rubin, E., & Wang, Z. (2016) · it - Information Technology · doi:10.1515/itit-2016-0011 · Cited by 25
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Davenport, C., Ussery, D. W., & Tümmler, B. (2010) · Photosynthesis Research · doi:10.1007/s11120-009-9515-2 · Cited by 17
Prajapati, A., Yogisharadhya, R., Mohanty, N. N., Mendem, S. K., Nizamuddin, A., Chanda, M. M., & Shivachandra, S. B. (2022) · Gene · doi:10.1016/j.gene.2022.146452 · Cited by 17
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Suzuki, T., Igarashi, K., Dohra, H., Someya, T., Takano, T., Harada, K., Omae, S., Hirai, H., Yano, K., & Kawagishi, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069681 · Cited by 17
Detecting Horizontally Transferred and Essential Genes Based on Dinucleotide Relative Abundance
Baran, R. H., & Ko, H. (2008) · DNA Research · doi:10.1093/dnares/dsn021 · Cited by 17
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Bouchot, J.-L., Trimble, W. L., Ditzler, G., Lan, Y., Essinger, S., & ROSEN, G. L. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-405926-9.00014-9 · Cited by 17
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Coutinho, T. J. D., Franco, G. R., & Lobo, F. P. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.04.005 · Cited by 17
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van Passel, M. W. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh115 · Cited by 17
Ghosh, T. S., Mohammed, M. H., Rajasingh, H., Chadaram, S., & Mande, S. S. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s13-s9 · Cited by 16
Bosi, E., Fondi, M., Maida, I., Perrin, E., de Pascale, D., Tutino, M. L., Parrilli, E., Giudice, A. L., Filloux, A., & Fani, R. (2015) · Hydrobiologia · doi:10.1007/s10750-015-2396-9 · Cited by 16
Motif depletion in bacteriophages infecting hosts with CRISPR systems
Kupczok, A., & Bollback, J. P. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-663 · Cited by 15
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Li, C., Fei, W., Zhao, Y., & Yu, X. (2016) · Applied Sciences · doi:10.3390/app6030063 · Cited by 15
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Wu, W., Zhou, Z., Riley, R. W., Abdulqader, M., Song, X., Kautsar, S. A., Egan, R. S., Hofmeyr, S. A., Liu, G., Goldhaber-Gordon, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.30.635558 · Cited by 19
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Weitschek, E., Cunial, F., & Felici, G. (2015) · BioData Mining · doi:10.1186/s13040-015-0073-1 · Cited by 14
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Yuan, J., Zhu, Q., & Liu, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084330 · Cited by 15
Dalevi, D., & Dubhashi, D. (2005) · Lecture notes in computer science · doi:10.1007/11557067_24 · Cited by 13
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Dehnert, M., Helm, W. E., & Hütt, M. ‐. (2006) · Physical Review E · doi:10.1103/physreve.74.021913 · Cited by 13
Xie, X., Chen, L., Yuan, J., Zheng, H., Zhang, L., Yu, X., Liu, X., Wei, C., & Qiu, G. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf278 · Cited by 12
Goussarov, G., Cleenwerck, I., Mysara, M., Leys, N., Monsieurs, P., Tahon, G., Carlier, A. L., Vandamme, P. A. R., & Houdt, R. V. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz964 · Cited by 12
Zhou, Y., Zheng, J., Wu, Y., Zhang, W., & Jin, J. (2020) · BMC Genomics · doi:10.1186/s12864-020-6597-x · Cited by 12
Sghaier, H., Thorvaldsen, S., & Malek, N. (2013) · Annals of Microbiology · doi:10.1007/s13213-013-0612-2 · Cited by 12
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Темиргалиевич, М. К., Klubin, A., Chelysheva, V. V., Selezneva, O. V., Акопян, Т. А., & Govorun, V. M. (2007) · Research in Microbiology · doi:10.1016/j.resmic.2007.01.002 · Cited by 12
Alsop, E. B., & Raymond, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067337 · Cited by 12
Bize, A., Midoux, C., Mariadassou, M., Schbath, S., Forterre, P., & Cunha, V. D. (2021) · BMC Genomics · doi:10.1186/s12864-021-07471-y · Cited by 14
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Mohammed, M. H., Chadaram, S., Komanduri, D., Ghosh, T. S., & Mande, S. S. (2011) · Journal of Biosciences · doi:10.1007/s12038-011-9105-2 · Cited by 11
Dyer, B. D., Kahn, M., & LeBlanc, M. D. (2007) · Archaea · doi:10.1155/2008/829730 · Cited by 11
Ding, X. L., Cheng, F., Cao, C., & Sun, X. S. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0753-3 · Cited by 11
Garcia, J. A. L., Bartumeus, F., Roche, D., Giraldo, J., Stanley, E., & Casamayor, E. O. (2008) · Genomics · doi:10.1016/j.ygeno.2008.03.001 · Cited by 11
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Godde, J. S., Baichoo, S., Mungloo-Dilmohamud, Z., & Jaufeerally‐Fakim, Y. (2018) · Microbiological Research · doi:10.1016/j.micres.2018.03.005 · Cited by 10
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Swain, M. (2013) · Procedia Computer Science · doi:10.1016/j.procs.2013.05.304 · Cited by 9
Abundant Oligonucleotides Common to Most Bacteria
Davenport, C., & Tümmler, B. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009841 · Cited by 8
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Skewes, A. D., & Welch, R. D. (2013) · PeerJ · doi:10.7717/peerj.127 · Cited by 9
Visualization of Pseudomonas genomic structure by abundant 8–14mer oligonucleotides
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Gori, F., Mavroeidis, D., Jetten, M. S. M., & Marchiori, E. (2011) · IEEE International Conference on Systems Biology · doi:10.1109/isb.2011.6033147 · Cited by 8
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Sangal, V., Nieminen, L., Tucker, N. P., & Hoskisson, P. A. (2014) · Methods in microbiology · doi:10.1016/bs.mim.2014.07.001 · Cited by 8
Sánchez, J. (2008) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.06.076 · Cited by 8
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Nasser, S., Breland, A. E., Harris, F. C., & Nicolescu, M. N. (2008) · Annual Meeting of the North American Fuzzy Information Processing Society (NAFIPS) · doi:10.1109/nafips.2008.4531252 · Cited by 8
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Nag, S., Chatterjee, R., Chaudhuri, K., & Chaudhuri, P. (2006) · Sadhana · doi:10.1007/bf02719776 · Cited by 8
Zhai, H., & Fukuyama, J. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010821 · Cited by 7
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Sánchez, J. (2011) · Bioinformation · doi:10.6026/97320630006327 · Cited by 7
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Tobar-Tosse, F., Rodríguez, A. C., Vélez, P. E., Zambrano, M. M., & Moreno, P. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059488 · Cited by 6
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Wang, Y., Brons, J. K., & van Elsas, J. D. (2021) · Microorganisms · doi:10.3390/microorganisms9102057 · Cited by 5
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Breland, A. E., Nasser, S., Schlauch, K. A., Nicolescu, M. N., & Harris, J. S. (2008) · Cited by 5
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Gupta, R. K., Singh, A. K., Bajaj, A., Khardenavis, A. A., & Purohit, H. J. (2022) · Journal of Basic Microbiology · doi:10.1002/jobm.202200323 · Cited by 4
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Ussery, D. W., Wassenaar, T. M., & Borini, S. (2008) · Computational biology · doi:10.1007/978-1-84800-255-5_8 · Cited by 4
Self-citationTetranucleotide usage highlights genomic heterogeneity among mycobacteriophages
Siranosian, B. A., Perera, S., Williams, E., Ye, C., de Graffenried, C. L., & Shank, P. R. (2015) · F1000Research · doi:10.12688/f1000research.6077.1 · Cited by 4
Yasuhara‐Bell, J., Arif, M., Busot, G. Y., Mann, R. A., Rodoni, B., & Stack, J. P. (2020) · Microorganisms · doi:10.3390/microorganisms8030366 · Cited by 4
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Meyerdierks, A., & Glöckner, F. O. (2010) · Springer eBooks · doi:10.1007/978-90-481-8639-6_2 · Cited by 5
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Singh, D. P., & Prabha, R. (2013) · JOURNAL OF ADVANCES IN BIOTECHNOLOGY · doi:10.24297/jbt.v3i3.5029 · Cited by 3
Bezuidt, O. K. I., Ganesan, H., Labuschange, P., Emmett, W., Pierneef, R., & Олег, Н. Л. (2011) · InTech eBooks · doi:10.5772/19296 · Cited by 2
Metadata
- Authors
- Pride, D. T., Meinersmann, R. J., Wassenaar, T. M., & Blaser, M. J.
- Affiliations
- Agricultural Research Service (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-01-14
- Volume
- 13
- Issue
- 2
- Pages
- 145-158
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC420360
- OpenAlex
- W2082521980
- Cited by
- 289
- References
- 49
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 9 · 2023: 4 · 2022: 31 · 2021: 10 · 2020: 9 · 2019: 11 · 2018: 7 · 2017: 12 · 2016: 11 · 2015: 27 · 2014: 11 · 2013: 21 · 2012: 11
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- Funders
- National Institutes of Health (5r01dk053707-06, CA68485)
- National Cancer Institute (CA68485, P30CA068485)
- National Institute of General Medical Sciences (R01 GM 63270, R01GM063270)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK 53707)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- prokaryotic genomes, phylogenetic signal, phylogenetic incongruence, 16S rRNA phylogeny, Markov chain analysis, bacterial evolution, genome-based phylogeny
- MeSH terms
- Chromosome Mapping, Chromosomes, Bacterial, DNA, Bacterial, Gram-Negative Bacteria, Gram-Positive Bacteria, Phylogeny, Plasmids, RNA, Bacterial, RNA, Ribosomal, 16S, Spirochaeta, Cluster Analysis, Genome, Bacterial, Microsatellite Repeats, DNA, Archaeal, RNA, Archaeal, Chromosomes, Archaeal, Genome, Archaeal, Gene Transfer, Horizontal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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