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GenoList: an integrated environment for comparative analysis of microbial genomes.

Lechat P, Hummel L, Rousseau S, Moszer I - Nucleic Acids Res. (2007)

Bottom Line: Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis.One key feature is the integration of the many tools accessible in the environment.As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.

View Article: PubMed Central - PubMed

Affiliation: Plate-forme Intégration et Analyse Génomiques, Pasteur Génopole Ile-de-France, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.

ABSTRACT
The multitude of bacterial genome sequences being determined has generated new requirements regarding the development of databases and graphical interfaces: these are needed to organize and retrieve biological information from the comparison of large sets of genomes. GenoList (http://genolist.pasteur.fr/GenoList) is an integrated environment dedicated to querying and analyzing genome data from bacterial species. GenoList inherits from the SubtiList database and web server, the reference data resource for the Bacillus subtilis genome. The data model was extended to hold information about relationships between genomes (e.g. protein families). The web user interface was designed to primarily take into account biologists' needs and modes of operation. Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis. One key feature is the integration of the many tools accessible in the environment. As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.

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Data and functionality integration in the GenoList environment. The first step consists in selecting species of interest (‘Organism selection’ panel). The central component of the application is the ‘Gene list’ panel (shown in the screen capture). Search outputs are presented there (‘Main queries’ and ‘Functional category’—blue rounded boxes), and results of sequence analysis tools (‘Search pattern’, ‘BLAST’, ‘DiffTool’ and ‘FindTarget’—yellow rounded boxes), which are displayed using specific layouts (e.g. BLAST reports), can also be converted to standard ‘Gene lists’. This panel acts as a hub since it gives access to many additional features (‘Gene page’, ‘Graphical display’ and ‘Export’), and it allows the user to bounce back to the sequence analysis tools from either one single gene or a subselection of the gene list. The screen capture illustrates the visualization of best hits of selected genes in a standard ‘Gene list’.
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Figure 1: Data and functionality integration in the GenoList environment. The first step consists in selecting species of interest (‘Organism selection’ panel). The central component of the application is the ‘Gene list’ panel (shown in the screen capture). Search outputs are presented there (‘Main queries’ and ‘Functional category’—blue rounded boxes), and results of sequence analysis tools (‘Search pattern’, ‘BLAST’, ‘DiffTool’ and ‘FindTarget’—yellow rounded boxes), which are displayed using specific layouts (e.g. BLAST reports), can also be converted to standard ‘Gene lists’. This panel acts as a hub since it gives access to many additional features (‘Gene page’, ‘Graphical display’ and ‘Export’), and it allows the user to bounce back to the sequence analysis tools from either one single gene or a subselection of the gene list. The screen capture illustrates the visualization of best hits of selected genes in a standard ‘Gene list’.

Mentions: Building upon these successive accomplishments, the GenoList multigenome environment was created: it consists of a relational database and a dynamic web application, aimed to take advantage of the multitude of published bacterial genomes to perform data analysis in a comparative genomics context. The development of GenoList was motivated by four key targets: (i) to organize microbial genome information in a specialized relational data schema, making it possible to implement complex relationships and subsequent queries; (ii) to supplement public genome data with original information, such as expertly curated annotations and comparative genomics data; (iii) to provide biologists with specific query and exploratory facilities conceived in an end-user-oriented fashion and (iv) to integrate the data content and the many search and analysis tools to seamlessly link up series of queries/responses (Figure 1). GenoList thus provides the user with an integrated environment that generates an added value compared to the initial data, both through the inclusion of original supplementary information and by enabling innovative functionalities for data study and extraction. GenoList is accessible at the URL http://genolist.pasteur.fr/GenoList.Figure 1.


GenoList: an integrated environment for comparative analysis of microbial genomes.

Lechat P, Hummel L, Rousseau S, Moszer I - Nucleic Acids Res. (2007)

Data and functionality integration in the GenoList environment. The first step consists in selecting species of interest (‘Organism selection’ panel). The central component of the application is the ‘Gene list’ panel (shown in the screen capture). Search outputs are presented there (‘Main queries’ and ‘Functional category’—blue rounded boxes), and results of sequence analysis tools (‘Search pattern’, ‘BLAST’, ‘DiffTool’ and ‘FindTarget’—yellow rounded boxes), which are displayed using specific layouts (e.g. BLAST reports), can also be converted to standard ‘Gene lists’. This panel acts as a hub since it gives access to many additional features (‘Gene page’, ‘Graphical display’ and ‘Export’), and it allows the user to bounce back to the sequence analysis tools from either one single gene or a subselection of the gene list. The screen capture illustrates the visualization of best hits of selected genes in a standard ‘Gene list’.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238853&req=5

Figure 1: Data and functionality integration in the GenoList environment. The first step consists in selecting species of interest (‘Organism selection’ panel). The central component of the application is the ‘Gene list’ panel (shown in the screen capture). Search outputs are presented there (‘Main queries’ and ‘Functional category’—blue rounded boxes), and results of sequence analysis tools (‘Search pattern’, ‘BLAST’, ‘DiffTool’ and ‘FindTarget’—yellow rounded boxes), which are displayed using specific layouts (e.g. BLAST reports), can also be converted to standard ‘Gene lists’. This panel acts as a hub since it gives access to many additional features (‘Gene page’, ‘Graphical display’ and ‘Export’), and it allows the user to bounce back to the sequence analysis tools from either one single gene or a subselection of the gene list. The screen capture illustrates the visualization of best hits of selected genes in a standard ‘Gene list’.
Mentions: Building upon these successive accomplishments, the GenoList multigenome environment was created: it consists of a relational database and a dynamic web application, aimed to take advantage of the multitude of published bacterial genomes to perform data analysis in a comparative genomics context. The development of GenoList was motivated by four key targets: (i) to organize microbial genome information in a specialized relational data schema, making it possible to implement complex relationships and subsequent queries; (ii) to supplement public genome data with original information, such as expertly curated annotations and comparative genomics data; (iii) to provide biologists with specific query and exploratory facilities conceived in an end-user-oriented fashion and (iv) to integrate the data content and the many search and analysis tools to seamlessly link up series of queries/responses (Figure 1). GenoList thus provides the user with an integrated environment that generates an added value compared to the initial data, both through the inclusion of original supplementary information and by enabling innovative functionalities for data study and extraction. GenoList is accessible at the URL http://genolist.pasteur.fr/GenoList.Figure 1.

Bottom Line: Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis.One key feature is the integration of the many tools accessible in the environment.As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.

View Article: PubMed Central - PubMed

Affiliation: Plate-forme Intégration et Analyse Génomiques, Pasteur Génopole Ile-de-France, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.

ABSTRACT
The multitude of bacterial genome sequences being determined has generated new requirements regarding the development of databases and graphical interfaces: these are needed to organize and retrieve biological information from the comparison of large sets of genomes. GenoList (http://genolist.pasteur.fr/GenoList) is an integrated environment dedicated to querying and analyzing genome data from bacterial species. GenoList inherits from the SubtiList database and web server, the reference data resource for the Bacillus subtilis genome. The data model was extended to hold information about relationships between genomes (e.g. protein families). The web user interface was designed to primarily take into account biologists' needs and modes of operation. Along with standard query and browsing capabilities, comparative genomics facilities are available, including subtractive proteome analysis. One key feature is the integration of the many tools accessible in the environment. As an example, it is straightforward to identify the genes that are specific to a group of bacteria, export them as a tab-separated list, get their protein sequences and run a multiple alignment on a subset of these sequences.

Show MeSH