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SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.

Lemoine F, Labedan B, Lespinet O - BMC Bioinformatics (2008)

Bottom Line: However, persistent synteny blocks are found when comparing more or less distant species.This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable.It is also possible to download sequences of genes belonging to these synteny blocks for further studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut de Génétique et Microbiologie, Université Paris Sud XI, CNRS UMR 8621, Bât, 400, 91405 Orsay Cedex, France. frederic.lemoine@igmors.u-psud.fr

ABSTRACT

Background: It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.

Results: After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.

Conclusion: SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.

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The two ways of using SynteView. In part A, the Web access mode connects the user to a Web service to retrieve synteny data stored in the SynteBase database . In part B, the local access mode connects the user to a local database containing the home-computed synteny data to be visualized.
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Figure 2: The two ways of using SynteView. In part A, the Web access mode connects the user to a Web service to retrieve synteny data stored in the SynteBase database . In part B, the local access mode connects the user to a local database containing the home-computed synteny data to be visualized.

Mentions: To implement SynteView, we applied an object oriented programming paradigm using the Java programming language [15]. In this way, SynteView may be run either as a Java Webstart application or as a local application (Fig. 2). In both cases, SynteView can be used to query SynteBase through a web service (web service mode), or used to query a local synteny database (loca access mode). The web service mode allows the user to visualize the precomputed data that are present in our version of SynteBase. To do so, SynteView connects to the SynteView web service to retrieve synteny data present in SynteBase. The local access mode will be useful for those who wish to work online, with home-made computed data. This mode requires the local installation of the Data Base Management System PostgreSQL [13], and the creation of a committed SynteBase-like database that must be populated with home made synteny data after applying the following mandatory requirements to visualize these data. SynteView requires information on proteins (identifier, coding strand, sequence, function, and length), genomes (species name, species name abbreviation, strain name, taxonomy), and synteny blocks (identifier of the blocks, and pairs of identifiers of orthologous proteins belonging to this block). Note that it does not matter how the data are organized in the underlying local database. SynteView parameters can be set to retrieve the data it needs. However, while SynteView is independent of the name of the selected fields, their order is of importance for correct functioning. Components required to set up a local database are described in detail in the Additional file 1. Once the custom-made database has been built, SynteView can connect to it, after the settings, including connection information (server, login, etc) and all the mandatory queries have been filled out.


SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.

Lemoine F, Labedan B, Lespinet O - BMC Bioinformatics (2008)

The two ways of using SynteView. In part A, the Web access mode connects the user to a Web service to retrieve synteny data stored in the SynteBase database . In part B, the local access mode connects the user to a local database containing the home-computed synteny data to be visualized.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667195&req=5

Figure 2: The two ways of using SynteView. In part A, the Web access mode connects the user to a Web service to retrieve synteny data stored in the SynteBase database . In part B, the local access mode connects the user to a local database containing the home-computed synteny data to be visualized.
Mentions: To implement SynteView, we applied an object oriented programming paradigm using the Java programming language [15]. In this way, SynteView may be run either as a Java Webstart application or as a local application (Fig. 2). In both cases, SynteView can be used to query SynteBase through a web service (web service mode), or used to query a local synteny database (loca access mode). The web service mode allows the user to visualize the precomputed data that are present in our version of SynteBase. To do so, SynteView connects to the SynteView web service to retrieve synteny data present in SynteBase. The local access mode will be useful for those who wish to work online, with home-made computed data. This mode requires the local installation of the Data Base Management System PostgreSQL [13], and the creation of a committed SynteBase-like database that must be populated with home made synteny data after applying the following mandatory requirements to visualize these data. SynteView requires information on proteins (identifier, coding strand, sequence, function, and length), genomes (species name, species name abbreviation, strain name, taxonomy), and synteny blocks (identifier of the blocks, and pairs of identifiers of orthologous proteins belonging to this block). Note that it does not matter how the data are organized in the underlying local database. SynteView parameters can be set to retrieve the data it needs. However, while SynteView is independent of the name of the selected fields, their order is of importance for correct functioning. Components required to set up a local database are described in detail in the Additional file 1. Once the custom-made database has been built, SynteView can connect to it, after the settings, including connection information (server, login, etc) and all the mandatory queries have been filled out.

Bottom Line: However, persistent synteny blocks are found when comparing more or less distant species.This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable.It is also possible to download sequences of genes belonging to these synteny blocks for further studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut de Génétique et Microbiologie, Université Paris Sud XI, CNRS UMR 8621, Bât, 400, 91405 Orsay Cedex, France. frederic.lemoine@igmors.u-psud.fr

ABSTRACT

Background: It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.

Results: After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.

Conclusion: SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.

Show MeSH