, Detecting overlapping coding sequences in virus genomes, BMC Bioinformatics, vol.7, issue.1, p.75, 2006.
DOI : 10.1186/1471-2105-7-75
URL : https://academic.oup.com/bioinformatics/article-pdf/21/3/282/652739/bti007.pdf
, The Complementary Strand of the Human T-Cell Leukemia Virus Type 1 RNA Genome Encodes a bZIP Transcription Factor That Down-Regulates Viral Transcription, Journal of Virology, vol.76, issue.24, pp.12813-12822, 2002.
DOI : 10.1128/JVI.76.24.12813-12822.2002
URL : https://hal.archives-ouvertes.fr/hal-00188771
, Mathematics for the Analysis of Algorithms, Birkhäuser, 1982.
DOI : 10.1007/978-0-8176-4729-2
URL : https://link.springer.com/content/pdf/bfm%3A978-0-8176-4729-2%2F1.pdf
, A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frames, Journal of Molecular Evolution, vol.3, issue.2, pp.181-189, 1995.
DOI : 10.1007/BF00167112
, Algorithm 447: efficient algorithms for graph manipulation, Communications of the ACM, vol.16, issue.6, pp.372-378, 1973.
DOI : 10.1145/362248.362272
, Origins of genes: "big bang" or continuous creation?, Proc. Natl, 1992.
DOI : 10.1073/pnas.89.20.9489
URL : http://www.pnas.org/content/89/20/9489.full.pdf
, Acad. Sci. USA, vol.89, pp.9489-9493
, Recent de novo origin of human protein-coding genes, Genome Research, vol.19, issue.10, pp.1752-1759, 2009.
DOI : 10.1101/gr.095026.109
, STABILITY AND EVOLUTION OF OVERLAPPING GENES, Evolution, vol.51, issue.3, pp.731-739, 2000.
DOI : 10.1007/BF02460081
, A simple method for displaying the hydropathic character of a protein, Journal of Molecular Biology, vol.157, issue.1, 1982.
DOI : 10.1016/0022-2836(82)90515-0
, J. Mol. Biol, vol.157, pp.105-132
, , 2012.
, antisense transcription is preferentially activated in primary monocyte-derived cells, J Virol, vol.86, pp.13785-13794, 2012.
, Birth and death of gene overlaps in vertebrates, BMC Evolutionary Biology, vol.7, issue.1, p.193, 2007.
DOI : 10.1186/1471-2148-7-193
, Human immunodeficiency virus may encode a novel protein on the genomic DNA plus strand, Science, vol.239, issue.4846, pp.1420-1422, 1988.
DOI : 10.1126/science.3347840
, Selection Pressure in Alternative Reading Frames, PLoS ONE, vol.14, issue.10, p.10, 2014.
DOI : 10.1371/journal.pone.0108768.s001
, Evolution of overlapping genes, Nature, vol.106, issue.5653, pp.532-535, 1978.
DOI : 10.1016/0022-2836(76)90275-8
, Overlapping Genes, Annual Review of Genetics, vol.17, issue.1, pp.499-525, 1983.
DOI : 10.1146/annurev.ge.17.120183.002435
, On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses, Journal of Molecular Evolution, vol.44, issue.6, pp.44-625, 1997.
DOI : 10.1007/PL00006185
, Detection of Signature Sequences in Overlapping Genes and Prediction of a Novel Overlapping Gene in Hepatitis G Virus, Journal of Molecular Evolution, vol.50, issue.3, pp.284-295, 2000.
DOI : 10.1007/s002399910033
, Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the, Gene Nursery " of Deltaretroviruses. Plos Computational Biology, vol.9, p.8, 2013.
DOI : 10.1371/journal.pcbi.1003162
URL : https://doi.org/10.1371/journal.pcbi.1003162
, A Dependent-Rates Model and an MCMC-Based Methodology for the Maximum-Likelihood Analysis of Sequences with Overlapping Reading Frames, Molecular Biology and Evolution, vol.18, issue.5, pp.763-776, 2001.
DOI : 10.1007/BF00175817
, Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation, Journal of Virology, vol.83, issue.20, pp.10719-10736, 2009.
DOI : 10.1128/JVI.00595-09
URL : http://jvi.asm.org/content/83/20/10719.full.pdf
, , 1985.
, Complete nucleotide sequence of the AIDS virus, HTLV-III, Nature, vol.313, pp.277-284
, Purifying and directional selection in overlapping prokaryotic genes, Trends in Genetics, vol.18, issue.5, pp.228-260, 2002.
DOI : 10.1016/S0168-9525(02)02649-5
, A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes, PLoS ONE, vol.17, issue.11, 2008.
DOI : 10.1371/journal.pone.0003996.t002
, 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, Journal of Molecular Evolution, vol.278, issue.Suppl 1, pp.5-6305, 2011.
DOI : 10.1074/jbc.M307417200
, Comparative study of overlapping genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.55, issue.3, pp.1205-1209, 2005.
DOI : 10.1099/ijs.0.63446-0
, Degeneracy of the information contained in amino acid sequences: Evidence from overlaid genes, Journal of Molecular Evolution, vol.272, issue.3, pp.245-252, 1979.
DOI : 10.1007/BF01739483
, The Ambush Hypothesis: Hidden Stop Codons Prevent Off-Frame Gene Reading, DNA and Cell Biology, vol.23, issue.10, pp.710-715, 2004.
DOI : 10.1089/dna.2004.23.701
, Degeneracy when DNA codes for overlapping genes, Mathematical Biosciences, vol.49, issue.1-2, p.16, 1980.
DOI : 10.1016/0025-5564(80)90107-8
, The Effect of Gene Overlapping on the Rate of RNA Virus Evolution, Molecular Biology and Evolution, vol.89, issue.8, pp.1916-1928, 2013.
DOI : 10.1016/j.ygeno.2006.12.007
, Protein constraints induced by multiframe encoding, Mathematical Biosciences, vol.49, issue.1-2, pp.17-26, 1980.
DOI : 10.1016/0025-5564(80)90108-X
, UniProt: a hub for protein information, The UniProt Consortium Nucleic Acids Res, vol.43, pp.204-212, 2015.
, Reviving an Old HIV-1 Gene: The HIV-1 Antisense Protein, Current HIV Research, vol.13, issue.2, pp.117-141, 2015.
DOI : 10.2174/1570162X12666141202125943
, 12 Antisense RNAs in bacteria and their genetic elements, 2002.
DOI : 10.1016/S0065-2660(02)46013-0
, Adv. Genet, vol.46, pp.361-398
, Missing genes in the annotation of prokaryotic genomes, BMC Bioinformatics, vol.11, issue.1, p.131, 2010.
DOI : 10.1186/1471-2105-11-131
, A Simple Method for Estimating the Strength of Natural Selection on Overlapping Genes, Genome Biology and Evolution, vol.95, issue.1, pp.381-390, 2015.
DOI : 10.1073/pnas.95.7.3708
, Computational Identification of Operons in Microbial Genomes, Genome Research, vol.12, issue.8, pp.1221-1230, 2002.
DOI : 10.1101/gr.200602
URL : http://genome.cshlp.org/content/12/8/1221.full.pdf
, ? The combination of constraints (7) and (8) (Tab. 2) in this order gives the 2 following di-peptide constraints, ) ó?W (H+Q) W (H+Q) ó? C (H+Q)
, ? The combination of constraints (8) and (7) gives: H (C+W) ó? Q (C+W) Q (C+W) ó? H (C+W)
, ? The double combination of constraint (7) gives: W (C+W) ó? H (H+Q) C (C+W) ó? Q (H+Q) and the double combination of constraint (8) gives the reciprocal constraints
, ? The combination of constraints (2) and (10) in this order gives: Y (D+E) ó? SY Y (F+K+L+N+R+S) ó?
, are removed from the right part of the constraints as they are forbidden di-peptides (Tab. 3), i.e. DY = 0 The (ordered) combination of Constraints (10) and (2) gives the reciprocal constraints
, ? The combination of constraints (8) and (10) in this order gives (the reverse order gives the reciprocal constraints
, ? The combination of constraints (7) and (10) in this order gives (the reverse order gives the reciprocal constraints
, )) lead to a di-peptide constraint that divides into two di-peptide constraints; and four combinations)) lead to three di-peptide constraints. This increases the total count of " non-null " constraints by 14. Moreover, one of the 10 2 constraints derived from the amino-acid constraints, YY ó? YY, is removed from the constraint set, as it is redundant with the two null constraints excluding dipeptide YY both in the reference and in the overlapping frame (Tab. 3), This results in 10 2 -1 + 14 = 113 non-null di-peptide constraints in frame -2, as found by our graph algorithm (Fig. 3) applied to " heptons