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Narcisse: a mirror view of conserved syntenies.

Courcelle E, Beausse Y, Letort S, Stahl O, Fremez R, Ngom-Bru C, Gouzy J, Faraut T - Nucleic Acids Res. (2007)

Bottom Line: New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects.The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes.The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Interactions Plantes Micro-organismes UMR 441/2594, INRA/CNRS and Laboratoire de Génétique Cellulaire UMR 444 INRA/ENVT, INRA, Centre de Recherches de Toulouse, 31326 Castanet Tolosan, France.

ABSTRACT
New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.

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Customisable layout and data access. Up to three genomes can be compared in the same view (one reference and two targets). The information content of the page is customizable by using the Display tab of the control panel. At any time the user can get the details of a gene element in the dynamic legend or retrieve corresponding sequences (gene/cds or proteins) using the contextual popup menu.
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Figure 4: Customisable layout and data access. Up to three genomes can be compared in the same view (one reference and two targets). The information content of the page is customizable by using the Display tab of the control panel. At any time the user can get the details of a gene element in the dynamic legend or retrieve corresponding sequences (gene/cds or proteins) using the contextual popup menu.

Mentions: The Narcisse comparative chromosome representation is based on a reference organism, displayed centrally, together with its associated annotation on which the identified conserved segments are anchored (either right or left, Figures 1, 3A and 4). Figure 1A shows a region of human chromosome 11 on which at least 7 segments have been identified as conserved with the rat genome. On each conserved segment, annotation is displayed according to the chromosome coordinate of this segment. As a result of the chaining algorithm, each conserved segment is made of segments of a lower level as exemplified by Figure 1B. The comparative representation of conserved segments can be adapted to the resolution level of the map under consideration; large conserved chromosomal segments are preferred at a cytogenetic scale while the representation of local sequence conservation is more informative when studying the vicinity of a set of genes (Figure 3B).Figure 3.


Narcisse: a mirror view of conserved syntenies.

Courcelle E, Beausse Y, Letort S, Stahl O, Fremez R, Ngom-Bru C, Gouzy J, Faraut T - Nucleic Acids Res. (2007)

Customisable layout and data access. Up to three genomes can be compared in the same view (one reference and two targets). The information content of the page is customizable by using the Display tab of the control panel. At any time the user can get the details of a gene element in the dynamic legend or retrieve corresponding sequences (gene/cds or proteins) using the contextual popup menu.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238891&req=5

Figure 4: Customisable layout and data access. Up to three genomes can be compared in the same view (one reference and two targets). The information content of the page is customizable by using the Display tab of the control panel. At any time the user can get the details of a gene element in the dynamic legend or retrieve corresponding sequences (gene/cds or proteins) using the contextual popup menu.
Mentions: The Narcisse comparative chromosome representation is based on a reference organism, displayed centrally, together with its associated annotation on which the identified conserved segments are anchored (either right or left, Figures 1, 3A and 4). Figure 1A shows a region of human chromosome 11 on which at least 7 segments have been identified as conserved with the rat genome. On each conserved segment, annotation is displayed according to the chromosome coordinate of this segment. As a result of the chaining algorithm, each conserved segment is made of segments of a lower level as exemplified by Figure 1B. The comparative representation of conserved segments can be adapted to the resolution level of the map under consideration; large conserved chromosomal segments are preferred at a cytogenetic scale while the representation of local sequence conservation is more informative when studying the vicinity of a set of genes (Figure 3B).Figure 3.

Bottom Line: New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects.The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes.The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire Interactions Plantes Micro-organismes UMR 441/2594, INRA/CNRS and Laboratoire de Génétique Cellulaire UMR 444 INRA/ENVT, INRA, Centre de Recherches de Toulouse, 31326 Castanet Tolosan, France.

ABSTRACT
New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.

Show MeSH
Related in: MedlinePlus