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. 2003 Jan 1;31(1):38-42.
doi: 10.1093/nar/gkg083.

Ensembl 2002: accommodating comparative genomics

M Clamp  1 , D Andrews, D Barker, P Bevan, G Cameron, Y Chen, L Clark, T Cox, J Cuff, V Curwen, T Down, R Durbin, E Eyras, J Gilbert, M Hammond, T Hubbard, A Kasprzyk, D Keefe, H Lehvaslaiho, V Iyer, C Melsopp, E Mongin, R Pettett, S Potter, A Rust, E Schmidt, S Searle, G Slater, J Smith, W Spooner, A Stabenau, J Stalker, E Stupka, A Ureta-Vidal, I Vastrik, E Birney
Affiliations

Ensembl 2002: accommodating comparative genomics

M Clamp et al. Nucleic Acids Res. .

Abstract

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

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Figures

Figure 1
Figure 1
Screenshot of Ensembl syntenyview. An overview of the synteny between human chromosome 6 and mouse is shown. The central chromosome is the human chromosome and the surrounding ones are the corresponding mouse chromosome. Ensembl clusters DNA–DNA matches into syntenic regions eliminating any paralogous DNA–DNA hits. Each segment is clickable and displays a menu showing the chromosomal coordinates of the match on both organisms and two extra options which take you to the contigview of one or other of the genomes. On the right hand side is a list of the potential orthologous proteins between the two genomes in the region identified by the red rectangle in left hand panel.
Figure 2
Figure 2
Screenshot of Apollo. This is a detailed synteny view in Apollo with one genome displayed on the top and the other genome on the bottom. In the middle are links between orthologous genes as identified by the Ensembl synteny generating software. The genes from both genomes are read from Ensembl databases and the orthologous gene pairs can either be read from an Ensembl compara database or from a flat file. The central panel can be used to scroll back and forth along the syntenic region or to centre the display on a particular region by clicking on one of the coloured matches. The top and bottom Apollo panels behave just as a normal, single Apollo panel and can be zoomed, scrolled, collapsed and also link out to a web page (as configured by the user).
See this image and copyright information in PMC

References

    1. Aparicio S., Chapman,J., Stupka,E., Putnam,N., Chia,J.M., Dehal,P., Christoffels,A., Rash,S., Hoon,S., Smit,A. et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science, 297, 1301–1310. - PubMed
    1. Hubbard T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38–41. - PMC - PubMed
    1. Birney E., Clamp,M.E. and Hubbard,T.J. (2002) Databases and tools for browsing genomes. Annu. Rev. Genome. Hum. Genet., 3, 293–310. - PubMed
    1. Rust A.G., Mongin,E. and Birney,E. (2002) Genome Annotation Techniques: New approaches and challenges. Drug Discov. Today, 7, S70–S76. - PubMed
    1. Tatusov R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631–637. - PubMed

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