Genomicus: Five genome browsers for comparative genomics in eukaryota

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Louis, Alexandra ^a,b,c   Muffato, Matthieu ^d   Crollius, Hugues Roest ^a,b,c  

^a PSL RESEARCH UNIVERSITY   (France)

^b INSERM   (France)

^c CNRS   (France)

^d EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLADISTICS; COMPARATIVE GENE MAPPING; DATA BASE; EUKARYOTE; GENE DUPLICATION; GENETIC ORGANIZATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; WEB BROWSER;

ANIMALS; DATABASES, NUCLEIC ACID; EUKARYOTA; EVOLUTION, MOLECULAR; GENE ORDER; GENOME, FUNGAL; GENOME, PLANT; GENOMICS; HUMANS; INTERNET; SEQUENCE ALIGNMENT; SOFTWARE; SYNTENY; VERTEBRATES;

EUKARYOTA; FUNGI; METAZOA; PROTISTA; VERTEBRATA;

EID: 84876554076     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1156     Document Type: Article

References (15)

1. Byrne, K.P. and Wolfe, K.H. (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res., 15, 1456-1461.
2. Pan, X., Stein, L. and Brendel, V. (2005) SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics, 21, 3461-3468.
3. Wang, H., Su, Y., Mackey, A.J., Kraemer, E.T. and Kissinger, J.C. (2006) SynView: a GBrowse-compatible approach to visualizing comparative genome data. Bioinformatics, 22, 2308-2309.
4. Courcelle, E., Beausse, Y., Letort, S., Stahl, O., Fremez, R., Ngom-Bru, C., Gouzy, J. and Faraut, T. (2008) Narcisse: a mirror view of conserved syntenies. Nucleic Acids Res., 36, D485-D490.
5. Lopez, M.D. and Samuelsson, T. (2011) eGOB: eukaryotic Gene Order Browser. Bioinformatics, 27, 1150-1151.
6. Revanna, K.V., Chiu, C.C., Bierschank, E. and Dong, Q. (2011) GSV: a web-based genome synteny viewer for customized data. BMC Bioinformatics, 12, 316.
7. Soderlund, C., Bomhoff, M. and Nelson, W.M. (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res., 39, e68.
8. Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N. et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res., 40, D1178-D1186.
9. Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
10. Kersey, P.J., Staines, D.M., Lawson, D., Kulesha, E., Derwent, P., Humphrey, J.C., Hughes, D.S.T., Keenan, S., Kerhornou, A., Koscielny, G. et al. (2012) Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res., 40, D91-D97.
11. Muffato, M., Louis, A., Poisnel, C.E. and Roest Crollius, H. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics, 26, 1119-1121.
12. Vilella, A.J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R. and Birney, E. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
13. Muffato, M. (2010) Reconstruction de génomes ancestraux chez les vertébrés, Ph.D. Thesis. Université d'Evry Val d'Essonne.
14. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
15. Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol., 20, 670-676.