-
1
-
-
0033214628
-
Heuristic approach to deriving models for gene finding
-
Besemer,J. and Borodovsky,M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res., 27, 3911-3920.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 3911-3920
-
-
Besemer, J.1
Borodovsky, M.2
-
2
-
-
0035875343
-
GeneMarkS: A self-training method for prediction of gene starts in microbial genomes: Implications for finding sequence motifs in regulatory regions
-
Besemer,J. et al. (2001) GeneMarkS: A self-training method for prediction of gene starts in microbial genomes: Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29 2607-2618.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2607-2618
-
-
Besemer, J.1
-
3
-
-
23044471144
-
Variability and conservation in hepatitis B virus core protein
-
Chain,B.M. and Myers,R. (2005) Variability and conservation in hepatitis B virus core protein. BMC Microbiol., 5.
-
(2005)
BMC Microbiol
, vol.5
-
-
Chain, B.M.1
Myers, R.2
-
4
-
-
34249856374
-
Comparative annotation of viral genomes with non-conserved gene structure
-
de Groot,S. et al. (2007) Comparative annotation of viral genomes with non-conserved gene structure. Bioinformatics, 23, 1080-1089.
-
(2007)
Bioinformatics
, vol.23
, pp. 1080-1089
-
-
de Groot, S.1
-
5
-
-
3843062475
-
Mapping sites of positive selection and amino acid diversification in the HIV genome
-
de Oliveira,T. et al. (2004) Mapping sites of positive selection and amino acid diversification in the HIV genome. Genetics, 167 1047-1058.
-
(2004)
Genetics
, vol.167
, pp. 1047-1058
-
-
de Oliveira, T.1
-
6
-
-
0032737463
-
Genealogical evidence for positive selection in the nef gene of HIV-1
-
de Zanotto,P. et al. (1999) Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics, 153, 1077-1089.
-
(1999)
Genetics
, vol.153
, pp. 1077-1089
-
-
de Zanotto, P.1
-
7
-
-
0028332808
-
New overlapping gene encoded by the cucumber mosaic virus genome
-
Ding,S.W. et al. (1994) New overlapping gene encoded by the cucumber mosaic virus genome. Virology, 198, 593-601.
-
(1994)
Virology
, vol.198
, pp. 593-601
-
-
Ding, S.W.1
-
9
-
-
36448970594
-
-
Felsenstein,J, 1989) PHYLIP, Phylogeny inference package Version 3.2, Cladistics, 5, 164-166
-
Felsenstein,J. (1989) PHYLIP - Phylogeny inference package (Version 3.2). Cladistics, 5, 164-166.
-
-
-
-
10
-
-
13844294363
-
Detecting overlapping coding sequences with pairwise alignments
-
Firth,A.E. and Brown,C.M. (2005) Detecting overlapping coding sequences with pairwise alignments. Bioinformatics, 21, 282-292.
-
(2005)
Bioinformatics
, vol.21
, pp. 282-292
-
-
Firth, A.E.1
Brown, C.M.2
-
11
-
-
33644837055
-
Detecting overlapping coding sequences in virus genomes
-
Firth,A.E. and Brown,C.M. (2006) Detecting overlapping coding sequences in virus genomes. BMC Bioinformatics, 7.
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Firth, A.E.1
Brown, C.M.2
-
12
-
-
0345490693
-
On dynamics of overlapping genes in bacterial genomes
-
Fukuda,Y. et al. (2003) On dynamics of overlapping genes in bacterial genomes. Gene, 323, 181-187.
-
(2003)
Gene
, vol.323
, pp. 181-187
-
-
Fukuda, Y.1
-
13
-
-
0036297144
-
Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products
-
Guyader,S. and Ducray,D.G. (2002) Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J. Gen. Virol., 83, 1799-1807.
-
(2002)
J. Gen. Virol
, vol.83
, pp. 1799-1807
-
-
Guyader, S.1
Ducray, D.G.2
-
14
-
-
0028922694
-
A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frame
-
Hein,J. and Støvlbæk,J. (1995) A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frame. J. Mol. Evol. 40, 181-189.
-
(1995)
J. Mol. Evol
, vol.40
, pp. 181-189
-
-
Hein, J.1
Støvlbæk, J.2
-
15
-
-
24944520911
-
Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes
-
Hughes,A.L. and Hughes,M.A.K. (2005) Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes. Virus Res., 113, 81-88.
-
(2005)
Virus Res
, vol.113
, pp. 81-88
-
-
Hughes, A.L.1
Hughes, M.A.K.2
-
16
-
-
0037358827
-
Detecting recombination in 4-taxa DNA sequence alignments with Bayesian Hidden Markov models and Markov chain Monte Carlo
-
Husmeier,D. and McGuire,G. (2003) Detecting recombination in 4-taxa DNA sequence alignments with Bayesian Hidden Markov models and Markov chain Monte Carlo. Mol. Biol. Evol., 20, 315-337.
-
(2003)
Mol. Biol. Evol
, vol.20
, pp. 315-337
-
-
Husmeier, D.1
McGuire, G.2
-
17
-
-
8744308029
-
Properties of overlapping genes are conserved across microbial genomes
-
Johnson,Z.I. and Chisholm,S. (2006) Properties of overlapping genes are conserved across microbial genomes. Genome Res., 14, 2268-2272.
-
(2006)
Genome Res
, vol.14
, pp. 2268-2272
-
-
Johnson, Z.I.1
Chisholm, S.2
-
18
-
-
0034331806
-
-
Koz1ov,N.N. (2000a) Overlapping genes and variability of the genetic code. Dokl. Biol. Sci., 375, 677-680.
-
Koz1ov,N.N. (2000a) Overlapping genes and variability of the genetic code. Dokl. Biol. Sci., 375, 677-680.
-
-
-
-
19
-
-
0034221509
-
Analysis of a set of overlapping genes
-
Kozlov,N.N. (2000b) Analysis of a set of overlapping genes. Dokl. Biochem., 373, 119-122.
-
(2000)
Dokl. Biochem
, vol.373
, pp. 119-122
-
-
Kozlov, N.N.1
-
20
-
-
12444259766
-
Overlapping genes in vertebrate genomes
-
Makalowska,I. et al. (2005) Overlapping genes in vertebrate genomes. Comput. Biol. Chem., 29, 1-12.
-
(2005)
Comput. Biol. Chem
, vol.29
, pp. 1-12
-
-
Makalowska, I.1
-
21
-
-
34447312039
-
Using HMMs and observed evolution to annotate viral genomes
-
Advance Access published online on April 13
-
McCauley,S. and Hein,J. (2006) Using HMMs and observed evolution to annotate viral genomes. Bioinformatics, Advance Access published online on April 13, 2006.
-
(2006)
Bioinformatics
-
-
McCauley, S.1
Hein, J.2
-
22
-
-
0345099561
-
Improving gene annotation of complete viral genomes
-
Mills,R. et al. (2003) Improving gene annotation of complete viral genomes. Nucleic Acids Res., 31, 7041-7055.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 7041-7055
-
-
Mills, R.1
-
23
-
-
21444455535
-
Dual multiple change-point model leads to more accurate recombination detection
-
Minin,V.N. et al. (2005) Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics, 21, 3034-3042.
-
(2005)
Bioinformatics
, vol.21
, pp. 3034-3042
-
-
Minin, V.N.1
-
24
-
-
0031030479
-
Constrained evolution with respect to gene overlap of Hepatitis B Virus
-
Mizokami,M. et al. (1997) Constrained evolution with respect to gene overlap of Hepatitis B Virus. J. Mol. Evol., 44 (Suppl. 1), 83-90.
-
(1997)
J. Mol. Evol
, vol.44
, Issue.SUPPL. 1
, pp. 83-90
-
-
Mizokami, M.1
-
25
-
-
33750332094
-
Molecular evolution of hepatitis B virus over 25 Years
-
Osiowy,C. et al. (2006) Molecular evolution of hepatitis B virus over 25 Years. J. Virol., 80, 10307-10314.
-
(2006)
J. Virol
, vol.80
, pp. 10307-10314
-
-
Osiowy, C.1
-
26
-
-
0033921799
-
Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus
-
Pavesi,A. (2000) Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus. J. Mol. Evol., 50, 284-295.
-
(2000)
J. Mol. Evol
, vol.50
, pp. 284-295
-
-
Pavesi, A.1
-
27
-
-
33645539406
-
Origin and evolution of overlapping genes in the family Microviridae
-
Pavesi,A. (2006) Origin and evolution of overlapping genes in the family Microviridae. J. Gen. Virol., 87, 1013-1017.
-
(2006)
J. Gen. Virol
, vol.87
, pp. 1013-1017
-
-
Pavesi, A.1
-
28
-
-
0030976687
-
On the informational content of overlapping genes in prokaryotic and eukaryotic viruses
-
Pavesi,A. et al. (1997) On the informational content of overlapping genes in prokaryotic and eukaryotic viruses. J. Mol. Evol., 44, 625-631.
-
(1997)
J. Mol. Evol
, vol.44
, pp. 625-631
-
-
Pavesi, A.1
-
29
-
-
0035035443
-
A dependent-rates model and an MCMC-bascd methodology for the maximum-likehhood analysis of sequences with overlapping reading frames
-
Pedersen,A.M. and Jensen,J.L. (2001) A dependent-rates model and an MCMC-bascd methodology for the maximum-likehhood analysis of sequences with overlapping reading frames. Mol. Biol. Evol., 18, 763-776.
-
(2001)
Mol. Biol. Evol
, vol.18
, pp. 763-776
-
-
Pedersen, A.M.1
Jensen, J.L.2
-
30
-
-
0037311782
-
Gene finding with a hidden Markov model of genome structure and evolution
-
Pedersen,J.S. and Hein,J. (2003) Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics, 19, 219-227.
-
(2003)
Bioinformatics
, vol.19
, pp. 219-227
-
-
Pedersen, J.S.1
Hein, J.2
-
31
-
-
0036575455
-
Purifying and directional selection in overlapping prokaryotic genes
-
Rogozin,I. et al. (2002) Purifying and directional selection in overlapping prokaryotic genes. Trends Genet., 18, 228-232.
-
(2002)
Trends Genet
, vol.18
, pp. 228-232
-
-
Rogozin, I.1
-
32
-
-
33749827106
-
Robust inference of positive selection from recombining coding sequences
-
Scheffler,K. et al. (2006) Robust inference of positive selection from recombining coding sequences. Bioinformatics, 22, 2493-2499.
-
(2006)
Bioinformatics
, vol.22
, pp. 2493-2499
-
-
Scheffler, K.1
-
33
-
-
0029095624
-
Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1)
-
Seibert,S. et al. (1995) Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol., 12, 803-813.
-
(1995)
Mol. Biol. Evol
, vol.12
, pp. 803-813
-
-
Seibert, S.1
-
34
-
-
1542537849
-
Combining phylogenetic and hidden Markov models in biosequence analysis
-
Siepel,A. and Haussler,D. (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol., 11, 413-428.
-
(2004)
J. Comput. Biol
, vol.11
, pp. 413-428
-
-
Siepel, A.1
Haussler, D.2
-
35
-
-
0025253821
-
Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1
-
Simmonds,P. et al. (1990) Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J. Virol., 64, 5840-5850.
-
(1990)
J. Virol
, vol.64
, pp. 5840-5850
-
-
Simmonds, P.1
-
36
-
-
0027273314
-
A small highly basic protein is encoded in overlapping reading frame within the P gene of vesicular stomatitis virus
-
Spiropoulou,C.F. and Nichol,S.T. (1993) A small highly basic protein is encoded in overlapping reading frame within the P gene of vesicular stomatitis virus. J. Virol., 67, 3103-3110.
-
(1993)
J. Virol
, vol.67
, pp. 3103-3110
-
-
Spiropoulou, C.F.1
Nichol, S.T.2
-
37
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Miura,R.M, ed, American Mathematic Society, Providence, pp
-
Tavaré,S. (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura,R.M. (ed.), Some Mathematical Questions in Biology DNA Sequence Analysis. American Mathematic Society, Providence, pp. 57-86.
-
(1986)
Some Mathematical Questions in Biology DNA Sequence Analysis
, pp. 57-86
-
-
Tavaré, S.1
-
38
-
-
0027968068
-
CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson,J.D. et al. (1994) CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
-
39
-
-
0036134765
-
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
-
Yang,Z.H. and Swanson,W.J. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol., 19, 49-57.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 49-57
-
-
Yang, Z.H.1
Swanson, W.J.2
-
40
-
-
0035050164
-
Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame
-
Walewski,J.L. et al. (2001) Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame. RNA, 7, 710-721.
-
(2001)
RNA
, vol.7
, pp. 710-721
-
-
Walewski, J.L.1
|