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References
Hood, L., Koop, B., Goverman, J. Hunkapiller, T. Model genomes: the benefits of analysing homologous human and mouse sequences, Trends Biotechnol., 1992, 10, pp.19–22.
Brenner, S., Elgar, G., Sandford, R., MacRae, A., Venkatesh, B. Aparicio, S. Characterization ofthe pufferfish (Fugu) genome as acompactmodel vertebrate genome, Nature, 1993, 366, pp.265–268.
Makalowski, W., Zhang, J.H. Boguski, M.S. Comparative analysis of 1196 orthologous mouse and human fill-length mrna and protein sequences, Genome Res., 1996, 6, pp.846–857.
Benson, D.A., Boguski, M.S., Lipman, D.J. Ostell, J. GenBank, Nucleic Acids Res., 1997, 25, pp.1–6.
Stoesser, G., Sterk, P., Tuli, M.A., Stoehr, P.J. Cameron, G.N. The EMBL Nucleotide Sequence Database, Nucleic Acids Res., 1997, 25, pp.7–13.
Duret, L., Mouchiroud, D. Gouy, M. HOVERGEN: a database of homologous vertebrate genes, Nucleic Acids Res., 1994, 22, pp.2360–2365.
Fitch, W.M. Distinguishing homologous from analogous proteins, Syst. Zool., 1970, 19, pp.99–113.
Doolittle, R.F. Convergent evolution: the need to be explicit, Trends Biochem. Sci., 1994, 19, pp.15–18.
Wootton, J.C. Federhen, S. Statistics of local complexity in amino acid sequences and sequence databases, Computers Chem., 1993, 17, pp.149–163.
Doolittle, R.F. Searching through sequence databases, Methods Enzymol., 1990, 183, pp.99–110.
Patthy, L. Modular exchange principlesin proteins, Curr. Opin. Struct. Biol., 1991, 1, pp.351–361.
Patthy, L. Introns and exons, Curr. Opin. Struct. Biol., 1994, 4, pp.383–392.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. Basic local alignment search tool, J. Mol. Biol., 1990, 215, pp.403–410.
Pearson, W.R. Lipman, D.J. Improved tools for biological sequence comparison, Proc. Natl. Acad. Sci. USA, 1988, 85, pp.2444–2448.
Li, W.H. Sadler, A. Low nucleotide diversity in man, Genetics, 1991, 129, pp.513–523.
Krawetz, S.A. Sequence errors in GenBank: a means to determine the accuracy of DNA sequence interpretation, Nucleic Acids Res., 1989, 17, pp.3951–3957.
Kristensen, T., Lopez, R. Prydz, H. An estimate of the sequencing error frequency in the DNA sequence databases, DNA Seq., 1992, 2, pp.343–346.
Lamperti, E.D., Kittelberger, J.M., Smith, T.F. Villa-Komaroff, L. Corruption of genomic databases with anomalous sequence, Nucleic Acids Res., 1992, 20, pp.2741–2747.
Sokal, R.R. Michener, C.D.A statistical method for evaluating systematic relationships, Univ. Kansas Sci. Bull., 1958, 28, pp.1409–1438.
Higgins, D.G., Bleasby, A.J. Fuchs, R. CLUSTAL V: imp roved software for multiple sequence alignment, Comp. Appl. Biosci., 1992, 8, pp.189–191.
Saitou, N. Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, 1987, 4, pp.406–425.
Gouy, M., Gautier, C., Attimonelli, M., Lanave, C. Di-Paola, G. ACNUC—a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage, Comp. Appl. Biosci., 1985, 1, pp.167–172.
Perriere, G., Gouy, M. Gojobori, T. NRSub: a non-redundant data base for the Bacillus subtilis genome, Nucleic Acids Res., 1994, 22, pp.5525–5529.
Perriere, G. Gouy, M. WWW-Query: An on-line retrieval system for biological sequence banks, Biochimie, 1996, 78, pp.364–369.
Mouchiroud, D., Gautier, C. Bernardi, G. Frequencies of synonymous substitution in mammals are gene-specific and correlated with frequencies of non-synonymous substitutions, J. Mol. Evol., 1995, 40, pp.107–113.
Hughes, A.L. Yeager, M. Comparative evolutionary rates of introns and exons in murine rodents, J. Mol. Evol., 1997, 45, pp.125–130.
Caccio, S., Zoubak, S., D’Onofrio, G. Bernardi, G. Nonrandom frequency patterns of synonymous substitutions in homologous mammalian genes, J. Mol. Evol., 1995, 40, pp.280–292.
Bernardi, G., Hughes, S. Mouchiroud, D. The major compositional transitions in the vertebrate genome, J. Mol. Evol., 1997, 44, pp.S44–S51.
Robinson, M., Gautier, C. Mouchiroud, D. Evolution of isochores in rodents, Mol. Biol. Evol., 1997, 14, pp.823–828.
Duret, L., Mouchiroud, D. Gautier, C. Statistic alanalysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores, J. Mol. Evol., 1995, 40, pp.308–317.
Ogata, H., Fujibuchi, W. Kanehisa, M. The size differences among mammalian introns are due to the accumulation of small deletions, FEBS Lett., 1996, 390, pp.99–103.
Graur, D., Duret, L. Gouy, M. Phylogenetic position of the order Lagomorpha (rabbits, hares and allies), Nature, 1996, 379, pp.333–335.
Graur, D., Gouy, M. Duret, L. Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata, Mol. Phylogenet. Evol., 1997, 7, pp. 195–200.
Hedges, S.B., Parker, P.H., Sibley, C.G. Kumar, S. Continental breakup and the ordinal diversification of birds and mammals, Nature, 1996, 381, pp.226–229.
Schuler, G.D., Epstein, J.A., Ohkawa, H. Kans, J.A. Entrez: molecular biology database and retrieval system, Methods Enzymol., 1996, 266, pp.141–162.
Mewes, H.W., Albermann, K., Heumann, K., Liebl, S. Pfeiffer, F. MIPS: A database for protein sequences, homology data and yeast genome information, Nucleic Acids Res., 1997, 25, pp.28–30.
Bairoch, A. Apweiler, R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL, Nucleic Acids Res., 1997, 25, pp.31–36.
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Duret, L., Perrière, G., Gouy, M. (2002). Hovergen: Comparative Analysis of Homologous Vertebrate Genes. In: Letovsky, S. (eds) Bioinformatics: Databases and Systems. Springer, Boston, MA. https://doi.org/10.1007/0-306-46903-0_3
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DOI: https://doi.org/10.1007/0-306-46903-0_3
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