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For: Firth AE, Brown CM. Detecting overlapping coding sequences with pairwise alignments. Bioinformatics 2004;21:282-92. [PMID: 15347574 DOI: 10.1093/bioinformatics/bti007] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Karlin DG. Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene. Viruses 2024;16:191. [PMID: 38399966 PMCID: PMC10891878 DOI: 10.3390/v16020191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024]  Open
2
Pavesi A. Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review. Genes (Basel) 2021;12:genes12060809. [PMID: 34073395 PMCID: PMC8227390 DOI: 10.3390/genes12060809] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022]  Open
3
Unconventional viral gene expression mechanisms as therapeutic targets. Nature 2021;593:362-371. [PMID: 34012080 DOI: 10.1038/s41586-021-03511-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
4
Du Y, Ji C, Liu T, Zhang W, Fang Q, Dong Q, Li M, Wang H, Chen Y, Ouyang K, Wei Z, Huang W. Identification of a novel protein in porcine astrovirus that is important for virus replication. Vet Microbiol 2021;255:108984. [PMID: 33684827 DOI: 10.1016/j.vetmic.2021.108984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/07/2021] [Indexed: 10/22/2022]
5
Orientation-dependent toxic effect of human papillomavirus type 33 long control region DNA in Escherichia coli cells. Virus Genes 2020;56:298-305. [PMID: 32246353 PMCID: PMC7220894 DOI: 10.1007/s11262-020-01754-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/20/2020] [Indexed: 11/15/2022]
6
Schlub TE, Buchmann JP, Holmes EC. A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences. Mol Biol Evol 2019;35:2572-2581. [PMID: 30099499 PMCID: PMC6188560 DOI: 10.1093/molbev/msy155] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
7
Kongari R, Rajaure M, Cahill J, Rasche E, Mijalis E, Berry J, Young R. Phage spanins: diversity, topological dynamics and gene convergence. BMC Bioinformatics 2018;19:326. [PMID: 30219026 PMCID: PMC6139136 DOI: 10.1186/s12859-018-2342-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]  Open
8
Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Wecko R, Simon S, Scherer S, Neuhaus K. A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting. BMC Evol Biol 2018;18:21. [PMID: 29433444 PMCID: PMC5810103 DOI: 10.1186/s12862-018-1134-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022]  Open
9
Kirby LE, Koslowsky D. Mitochondrial dual-coding genes in Trypanosoma brucei. PLoS Negl Trop Dis 2017;11:e0005989. [PMID: 28991908 PMCID: PMC5650466 DOI: 10.1371/journal.pntd.0005989] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/20/2017] [Accepted: 09/23/2017] [Indexed: 12/31/2022]  Open
10
Lim CS, Brown CM. Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element. RNA Biol 2016;13:743-7. [PMID: 27031749 DOI: 10.1080/15476286.2016.1166330] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
11
Woo PCY, Lau SKP, Teng JLL, Tsang AKL, Joseph S, Xie J, Jose S, Fan RYY, Wernery U, Yuen KY. A novel astrovirus from dromedaries in the Middle East. J Gen Virol 2015;96:2697-2707. [PMID: 26296576 DOI: 10.1099/jgv.0.000233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
12
Batista ARS, Nicolini C, Rodrigues KB, Melo FL, Vasques RM, de Macêdo MA, Inoue-Nagata AK, Nagata T. Unique RNA 2 sequences of two Brazilian isolates of Pepper ringspot virus, a tobravirus. Virus Genes 2014;49:169-73. [DOI: 10.1007/s11262-014-1066-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
13
Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses. PLoS Comput Biol 2013;9:e1003162. [PMID: 23966842 PMCID: PMC3744397 DOI: 10.1371/journal.pcbi.1003162] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 06/13/2013] [Indexed: 12/24/2022]  Open
14
Kawano Y, Neeley S, Adachi K, Nakai H. An experimental and computational evolution-based method to study a mode of co-evolution of overlapping open reading frames in the AAV2 viral genome. PLoS One 2013;8:e66211. [PMID: 23826091 PMCID: PMC3691236 DOI: 10.1371/journal.pone.0066211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/07/2013] [Indexed: 02/07/2023]  Open
15
Sabath N, Wagner A, Karlin D. Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol 2012;29:3767-80. [PMID: 22821011 PMCID: PMC3494269 DOI: 10.1093/molbev/mss179] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
16
Sabath N, Morris JS, Graur D. Is there a twelfth protein-coding gene in the genome of influenza A? A selection-based approach to the detection of overlapping genes in closely related sequences. J Mol Evol 2011;73:305-15. [PMID: 22187135 DOI: 10.1007/s00239-011-9477-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 12/02/2011] [Indexed: 02/06/2023]
17
Norovirus regulation of the innate immune response and apoptosis occurs via the product of the alternative open reading frame 4. PLoS Pathog 2011;7:e1002413. [PMID: 22174679 PMCID: PMC3234229 DOI: 10.1371/journal.ppat.1002413] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 10/12/2011] [Indexed: 12/25/2022]  Open
18
Baranov PV, Wills NM, Barriscale KA, Firth AE, Jud MC, Letsou A, Manning G, Atkins JF. Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). RNA Biol 2011;8:637-47. [PMID: 21593603 PMCID: PMC3225980 DOI: 10.4161/rna.8.4.15395] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 03/03/2011] [Accepted: 03/04/2011] [Indexed: 12/14/2022]  Open
19
Sabath N, Graur D. Detection of functional overlapping genes: simulation and case studies. J Mol Evol 2010;71:308-16. [PMID: 20820768 DOI: 10.1007/s00239-010-9386-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 07/26/2010] [Indexed: 12/16/2022]
20
Firth AE, Atkins JF. Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning. Virol J 2010;7:17. [PMID: 20100346 PMCID: PMC2832772 DOI: 10.1186/1743-422x-7-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 01/25/2010] [Indexed: 11/10/2022]  Open
21
Firth AE, Atkins JF. Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene. Virol J 2009;6:222. [PMID: 20017924 PMCID: PMC2805633 DOI: 10.1186/1743-422x-6-222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 12/17/2009] [Indexed: 11/23/2022]  Open
22
Clifford M, Twigg J, Upton C. Evidence for a novel gene associated with human influenza A viruses. Virol J 2009;6:198. [PMID: 19917120 PMCID: PMC2780412 DOI: 10.1186/1743-422x-6-198] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 11/16/2009] [Indexed: 02/06/2023]  Open
23
Firth AE, Wang QS, Jan E, Atkins JF. Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses. Virol J 2009;6:193. [PMID: 19895695 PMCID: PMC2777877 DOI: 10.1186/1743-422x-6-193] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 11/06/2009] [Indexed: 02/09/2023]  Open
24
Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol 2009;18:20-9. [PMID: 19896852 DOI: 10.1016/j.tim.2009.10.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 10/14/2009] [Accepted: 10/19/2009] [Indexed: 12/13/2022]
25
Firth AE, Bekaert M, Baranov PV. Computational Resources for Studying Recoding. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-0-387-89382-2_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
26
Firth AE, Atkins JF. A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product. Virol J 2009;6:136. [PMID: 19737402 PMCID: PMC2749830 DOI: 10.1186/1743-422x-6-136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2009] [Accepted: 09/08/2009] [Indexed: 11/23/2022]  Open
27
Firth AE, Atkins JF. Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses. Virol J 2009;6:32. [PMID: 19292925 PMCID: PMC2666654 DOI: 10.1186/1743-422x-6-32] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 03/17/2009] [Indexed: 01/10/2023]  Open
28
Firth AE, Atkins JF. Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene. Arch Virol 2008;153:1379-83. [PMID: 18535758 DOI: 10.1007/s00705-008-0119-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 04/16/2008] [Indexed: 11/29/2022]
29
Firth AE, Atkins JF. Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene. Virol J 2008;5:62. [PMID: 18492230 PMCID: PMC2409309 DOI: 10.1186/1743-422x-5-62] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 05/20/2008] [Indexed: 11/10/2022]  Open
30
Firth AE. Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene. Virol J 2008;5:48. [PMID: 18489030 PMCID: PMC2373779 DOI: 10.1186/1743-422x-5-48] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 04/14/2008] [Indexed: 11/25/2022]  Open
31
An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci U S A 2008;105:5897-902. [PMID: 18408156 DOI: 10.1073/pnas.0800468105] [Citation(s) in RCA: 579] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
32
Panjaworayan N, Roessner SK, Firth AE, Brown CM. HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences. Virol J 2007;4:136. [PMID: 18086305 PMCID: PMC2235840 DOI: 10.1186/1743-422x-4-136] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 12/17/2007] [Indexed: 12/28/2022]  Open
33
McCauley S, de Groot S, Mailund T, Hein J. Annotation of selection strengths in viral genomes. Bioinformatics 2007;23:2978-86. [PMID: 17921171 DOI: 10.1093/bioinformatics/btm472] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
34
Belshaw R, Pybus OG, Rambaut A. The evolution of genome compression and genomic novelty in RNA viruses. Genome Res 2007;17:1496-504. [PMID: 17785537 PMCID: PMC1987338 DOI: 10.1101/gr.6305707] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
35
de Groot S, Mailund T, Hein J. Comparative annotation of viral genomes with non-conserved gene structure. Bioinformatics 2007;23:1080-9. [PMID: 17341494 DOI: 10.1093/bioinformatics/btm078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
36
McCauley S, Hein J. Using hidden Markov models and observed evolution to annotate viral genomes. Bioinformatics 2006;22:1308-16. [PMID: 16613911 DOI: 10.1093/bioinformatics/btl092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
37
Allen MJ, Schroeder DC, Donkin A, Crawfurd KJ, Wilson WH. Genome comparison of two Coccolithoviruses. Virol J 2006;3:15. [PMID: 16553948 PMCID: PMC1440845 DOI: 10.1186/1743-422x-3-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Accepted: 03/22/2006] [Indexed: 11/17/2022]  Open
38
Firth AE, Brown CM. Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics 2006;7:75. [PMID: 16483358 PMCID: PMC1395342 DOI: 10.1186/1471-2105-7-75] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 02/16/2006] [Indexed: 11/10/2022]  Open
39
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447509 DOI: 10.1002/cfg.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
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