{"id":185801,"date":"2025-11-17T19:26:12","date_gmt":"2025-11-17T19:26:12","guid":{"rendered":"https:\/\/www.europesays.com\/ie\/185801\/"},"modified":"2025-11-17T19:26:12","modified_gmt":"2025-11-17T19:26:12","slug":"unexplored-diversity-and-molecular-genetic-signatures-of-chimallin-and-phuz-encoding-phages-bmc-genomics","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/ie\/185801\/","title":{"rendered":"Unexplored diversity and molecular genetic signatures of chimallin and phuz encoding phages | BMC Genomics"},"content":{"rendered":"
  • \n

    Yuan Y, Gao M. Jumbo bacteriophages: an overview. Front Microbiol. 2017;8:403.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, et al. Clades of huge phages from across earth\u2019s ecosystems. Nature. 2020;578:425\u201331.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chaikeeratisak V, Nguyen K, Khanna K, Brilot AF, Erb ML, Coker JK, et al. Assembly of a nucleus-like structure during viral replication in bacteria. Science. 2017;355:194\u20137.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, et al. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature. 2022;608:429\u201335.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, et al. A bacteriophage nucleus-like compartment shields DNA from crispr nucleases. Nature. 2020;577:244\u20138.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nguyen KT, Sugie J, Khanna K, Egan ME, Birkholz EA, Lee J, et al. Selective transport of fluorescent proteins into the phage nucleus. PLoS One. 2021;16:e0251429.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chaikeeratisak V, Khanna K, Nguyen KT, Egan ME, Enustun E, Armbruster E, et al. Subcellular organization of viral particles during maturation of nucleus-forming jumbo phage. Sci Adv. 2022;8:eabj9670.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Krylov V, Bourkaltseva M, Pleteneva E, Shaburova O, Krylov S, Karaulov A, et al. Phage phikz-the first of giants. Viruses. 2021. https:\/\/doi.org\/10.3390\/v13020149<\/a><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wu W, Thomas JA, Cheng N, Black LW, Steven AC. Bubblegrams reveal the inner body of bacteriophage phikz. Science. 2012;335:182.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Thomas JA, Weintraub ST, Wu W, Winkler DC, Cheng N, Steven AC, et al. Extensive proteolysis of head and inner body proteins by a morphogenetic protease in the giant pseudomonas aeruginosa phage phikz. Mol Microbiol. 2012;84:324\u201339.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, et al. Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection. Cell Host Microbe. 2024;32(1050\u201358):e7.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gerovac M, Chihara K, Wicke L, Bottcher B, Lavigne R, Vogel J. Phage proteins target and co-opt host ribosomes immediately upon infection. Nat Microbiol. 2024;9:787\u2013800.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Morgan CJ, Enustun E, Armbruster EG, Birkholz EA, Prichard A, Forman T, et al. An essential and highly selective protein import pathway encoded by nucleus-forming phage. Proc Natl Acad Sci U S A. 2024;121:e2321190121.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Malukhina K, et al. A phage nucleus-associated rna-binding protein is required for jumbo phage infection. Nucleic Acids Res. 2024;52:4440\u201355.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chaikeeratisak V, Khanna K, Nguyen KT, Sugie J, Egan ME, Erb ML, et al. Viral capsid trafficking along treadmilling tubulin filaments in bacteria. Cell. 2019;177(1771\u201380):e12.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Malone LM, Warring SL, Jackson SA, Warnecke C, Gardner PP, Gumy LF, et al. A jumbo phage that forms a nucleus-like structure evades crispr-cas DNA targeting but is vulnerable to type iii rna-based immunity. Nat Microbiol. 2020;5:48\u201355.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Birkholz EA, Laughlin TG, Armbruster E, Suslov S, Lee J, Wittmann J, et al. A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in e. Coli. Cell Rep. 2022;40:111179.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, et al. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage ray. Cell Rep. 2023;42:112432.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, et al. A network-based integrated framework for predicting virus-prokaryote interactions. NAR Genom Bioinform. 2020;2:lqaa044.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li Y, Guan J, Hareendranath S, Crawford E, Agard DA, Makarova KS et al. A family of novel immune systems targets early infection of nucleus-forming jumbo phages. bioRxiv. 2022:2022.09.17.508391. https:\/\/doi.org\/10.1101\/2022.09.17.508391<\/a>.<\/p>\n<\/li>\n

  • \n

    Wakui D, Nagashima G, Otsuka Y, Takada T, Ueda T, Tanaka Y, et al. A case of meningitis due to neisseria subflava after ventriculostomy. J Infect Chemother. 2012;18:115\u20138.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lee MR, Sheng WH, Hung CC, Yu CJ, Lee LN, Hsueh PR. Mycobacterium abscessus complex infections in humans. Emerg Infect Dis. 2015;21:1638\u201346.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shkoporov AN, Hill C. Bacteriophages of the human gut: The \u201cknown unknown\u201d of the microbiome. Cell Host Microbe. 2019;25:195\u2013209.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Prichard A, Sy A, Meyer J, Villa E, Pogliano J. Erwinia phage asesino is a nucleus-forming phage that lacks phuz. Sci Rep. 2025;15:1692.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chaikeeratisak V, Nguyen K, Egan ME, Erb ML, Vavilina A, Pogliano J. The phage nucleus and tubulin spindle are conserved among large pseudomonas phages. Cell Rep. 2017;20:1563\u201371.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mann S, Chen YP. Bacterial genomic g+c composition-eliciting environmental adaptation. Genomics. 2010;95:7\u201315.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kakasis A, Panitsa G. Bacteriophage therapy as an alternative treatment for human infections. A comprehensive review. Int J Antimicrob Agents. 2019;53:16\u201321.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, et al. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol. 2019;4:693\u2013700.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, et al. Reproductive mode and the evolution of genome size and structure in caenorhabditis nematodes. PLoS Genet. 2015;11:e1005323.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Felsenstein J. The evolutionary advantage of recombination. Genetics. 1974;78:737\u201356.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Murphy J, Klumpp J, Mahony J, O\u2019Connell-Motherway M, Nauta A, van Sinderen D. Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity. BMC Genomics. 2014;15:831.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, et al. Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems. Nature. 2022;609:144\u201350.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Leavitt A, Yirmiya E, Amitai G, Lu A, Garb J, Herbst E, et al. Viruses inhibit Tir gcadpr signalling to overcome bacterial defence. Nature. 2022;611:326\u201331.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, et al. Specific interaction of novel friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types. J Virol. 2021. https:\/\/doi.org\/10.1128\/JVI.01714-20<\/a>.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang B, Zheng J, Yin Y. Acafinder: genome mining for anti-crispr-associated genes. mSystems. 2022;7:e0081722.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hobbs SJ, Wein T, Lu A, Morehouse BR, Schnabel J, Leavitt A, et al. Phage anti-cbass and anti-pycsar nucleases subvert bacterial immunity. Nature. 2022;605:522\u20136.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Azam AH, Chihara K, Kondo K, Nakamura T, Ojima S, Tamura A et al. Viruses encode trna and anti-retron to evade bacterial immunity. bioRxiv. 2023:2023.03.15.532788. https:\/\/doi.org\/10.1101\/2023.03.15.532788<\/a>.<\/p>\n<\/li>\n

  • \n

    Murphy KC, Lewis LJ. Properties of Escherichia coli expressing bacteriophage p22 abc (anti-recbcd) proteins, including inhibition of chi activity. J Bacteriol. 1993;175(6):1756\u201366.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Camargo AP, Nayfach S, Chen IA, Palaniappan K, Ratner A, Chu K, et al. Img\/vr v4: An expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res. 2023;51:D733\u201343.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Weinheimer AR, Aylward FO. Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages. ISME J. 2022;16(6):1657\u201367.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nayfach S, Paez-Espino D, Call L, Low SJ, Sberro H, Ivanova NN, et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol. 2021;6:960\u201370.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Massive expansion of human gut bacteriophage diversity. Cell. 2021;184(1098\u2013109):e9.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Benler S, Yutin N, Antipov D, Rayko M, Shmakov S, Gussow AB, et al. Thousands of previously unknown phages discovered in whole-community human gut metagenomes. Microbiome. 2021;9:78.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Terzian P, Olo Ndela E, Galiez C, Lossouarn J, Perez Bucio RE, Mom R, et al. Phrog: Families of prokaryotic virus proteins clustered using remote homology. NAR Genom Bioinform. 2021;3:lqab067.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic virus orthologous groups (pvogs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 2017;45:D491-8.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. Eggnog 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44:D286-93.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The pfam protein families database in 2019. Nucleic Acids Res. 2019;47:D427\u201332.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. Kofamkoala: kegg ortholog assignment based on profile hmm and adaptive score threshold. Bioinformatics. 2020;36:2251\u20132.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Katoh K, Standley DM. Mafft multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772\u201380.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Eddy SR. Accelerated profile hmm searches. PLoS Comput Biol. 2011;7:e1002195.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shen W, Le S, Li Y, Hu F. Seqkit: a cross-platform and ultrafast toolkit for fasta\/q file manipulation. PLoS One. 2016;11:e0163962.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science. 2021;373:871\u20136.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    van Kempen M, Kim SS, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, et al. Fast and accurate protein structure search with foldseek. Nat Biotechnol. 2024;42(2):243\u20136.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Olm MR, Brown CT, Brooks B, Banfield JF. Drep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864\u20138.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. Checkv assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2021;39:578\u201385.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kieft K, Zhou Z, Anantharaman K. Vibrant: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8:90.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tesson F, Huiting E, Wei L, Ren J, Johnson M, Planel R, et al. Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements. Nucleic Acids Res. 2025. https:\/\/doi.org\/10.1093\/nar\/gkae1171<\/a>.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bin Jang H, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol. 2019;37:632\u20139.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Neron B, et al. Crisprcasfinder, an update of crisrfinder, includes a portable version, enhanced performance and integrates search for cas proteins. Nucleic Acids Res. 2018;46:W246\u201351.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. Blast+: architecture and applications. BMC Bioinformatics. 2009;10:421.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Luo XQ, Wang P, Li JL, Ahmad M, Duan L, Yin LZ, et al. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. Microbiome. 2022;10:190.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Howell AA, Versoza CJ, Pfeifer SP. Computational host range prediction-the good, the bad, and the ugly. Virus Evol. 2024;10:vead083.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shang J, Sun Y. Cherry: a computational method for accurate prediction of virus-prokaryotic interactions using a graph encoder-decoder model. Brief Bioinform. 2022. https:\/\/doi.org\/10.1093\/bib\/bbac182<\/a>.<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Amgarten D, Iha BKV, Piroupo CM, da Silva AM, Setubal JC. Vhulk, a new tool for bacteriophage host prediction based on annotated genomic features and neural networks. PHAGE. 2022;3:204\u201312.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972\u20133.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. Iq-tree 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530\u20134.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fu L, Niu B, Zhu Z, Wu S, Li W. Cd-hit: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150\u20132.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Price MN, Dehal PS, Arkin AP. Fasttree 2\u2013approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068\u20139.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ding W, Baumdicker F, Neher RA. Panx: pan-genome analysis and exploration. Nucleic Acids Res. 2018;46:e5.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chan PP, Lowe TM. Trnascan-se: Searching for trna genes in genomic sequences. Methods Mol Biol. 2019;1962:1\u201314.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:1009\u201310.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lu J, Salzberg SL. Skewit: the skew index test for large-scale GC skew analysis of bacterial genomes. PLoS Comput Biol. 2020;16:e1008439.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357\u20139.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. 2019;176(649\u201362):e20.<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Morais S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, et al. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science. 2024;383:eadj9223.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li R, Wang Y, Hu H, Tan Y, Ma Y. Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut. Nat Commun. 2022;13:7978.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Li D, Liu CM, Luo R, Sadakane K, Lam TW. Megahit: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph. Bioinformatics. 2015;31:1674\u20136.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kolmogorov M, Raney B, Paten B, Pham S. Ragout-a reference-assisted assembly tool for bacterial genomes. Bioinformatics. 2014;30:i302-9.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen T, Liu YX, Huang L. Imagegp: an easy-to-use data visualization web server for scientific researchers. Imeta. 2022;1:e5.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27:431\u20132.<\/p>\n

    PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Letunic I, Bork P. Interactive tree of life (itol) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242\u20135.<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Yuan Y, Gao M. Jumbo bacteriophages: an overview. Front Microbiol. 2017;8:403. PubMed\u00a0 PubMed Central\u00a0 Google Scholar\u00a0 Al-Shayeb B,…\n","protected":false},"author":2,"featured_media":185802,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[77],"tags":[2569,104499,104500,18,910,19,17,3544,9693,6720,104497,6719,104498,3549,133],"class_list":{"0":"post-185801","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-animal-genetics-and-genomics","9":"tag-anti-defense-system","10":"tag-earths-ecosystems","11":"tag-eire","12":"tag-general","13":"tag-ie","14":"tag-ireland","15":"tag-life-sciences","16":"tag-microarrays","17":"tag-microbial-genetics-and-genomics","18":"tag-nucleus-forming-phages","19":"tag-plant-genetics-and-genomics","20":"tag-protein-nucleus-shell","21":"tag-proteomics","22":"tag-science"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@ie\/115566689801806269","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/185801","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=185801"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/185801\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/185802"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=185801"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=185801"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=185801"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}