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HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.

Puigbò P, Romeu A, Garcia-Vallvé S - Nucleic Acids Res. (2007)

Bottom Line: This information can also be accessed using a search engine.Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set.The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), c/Marcel-li Domingo, s/n. Campus Sescelades, 43007 Tarragona, Spain. ppuigbo@urv.cat

ABSTRACT
The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set. The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes. The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB.

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Outputs provided from the HEG-DB: (a) ‘Genomes consult’ shows the list of all the genomes available in the database. In this section, users can select one or more genomes to see the statistical parameters (including the codon usage correspondence analysis plot used to predict translational selection) of the selected genomes. (b) The statistical and functional information available in each gene is accessible by a global consult of a specific genome or by a search engine. This section includes the CAI value of each gene. (c) List of predicted highly expressed genes in each genome. This section includes functional and positional information about each predicted gene. (d) The metabolic pathways, which involve highly expressed genes can be viewed through the ‘pathway tools overview expression viewer’ from the BioCyc database. In addition, this tool can be used to mark all genes according to their CAI on the pathway maps.
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Figure 1: Outputs provided from the HEG-DB: (a) ‘Genomes consult’ shows the list of all the genomes available in the database. In this section, users can select one or more genomes to see the statistical parameters (including the codon usage correspondence analysis plot used to predict translational selection) of the selected genomes. (b) The statistical and functional information available in each gene is accessible by a global consult of a specific genome or by a search engine. This section includes the CAI value of each gene. (c) List of predicted highly expressed genes in each genome. This section includes functional and positional information about each predicted gene. (d) The metabolic pathways, which involve highly expressed genes can be viewed through the ‘pathway tools overview expression viewer’ from the BioCyc database. In addition, this tool can be used to mark all genes according to their CAI on the pathway maps.

Mentions: The information about genes and genomes is stored in a MySQL database that can be accessed through a series of PHP web pages. The current version of the database contains information about almost 200 genomes under translational selection. The HTML interface is divided into four sections (Figure 1): (i) The first section contains information about the genomes under translational selection, including links to some statistical parameters for these genomes, such as mean and standard deviations of total and positional G + C content, codon usage per thousand, relative synonymous codon usage and amino acid content. This section also includes the correspondence analysis plots of the relative synonymous codon usage for all the genes of the genomes used to predict translational selection. (ii) The second section contains the list of the predicted highly expressed genes for all of the genomes under translational selection with their functional and positional information. (iii) Since the definition of highly expressed genes is relative and depends on the limits, for each gene in the genomes under translational selection, we have included its CAI value. This information can also be accessed via a search engine that searches for gene names or keywords for a specific organism and taxa. (iv) To see the metabolic capabilities of genomes under translational selection, the fourth section enables all the genes in a genome to be represented according to their CAI value on a metabolic map, using the Pathway Tools Omics Viewer from BioCyc (22,23). The group of predicted highly expressed genes can be located separately on the metabolic pathway map of each genome. This last section makes a detailed functional analysis of the group of highly expressed genes and the preferred metabolic pathways in each genome under translational selection.Figure 1.


HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.

Puigbò P, Romeu A, Garcia-Vallvé S - Nucleic Acids Res. (2007)

Outputs provided from the HEG-DB: (a) ‘Genomes consult’ shows the list of all the genomes available in the database. In this section, users can select one or more genomes to see the statistical parameters (including the codon usage correspondence analysis plot used to predict translational selection) of the selected genomes. (b) The statistical and functional information available in each gene is accessible by a global consult of a specific genome or by a search engine. This section includes the CAI value of each gene. (c) List of predicted highly expressed genes in each genome. This section includes functional and positional information about each predicted gene. (d) The metabolic pathways, which involve highly expressed genes can be viewed through the ‘pathway tools overview expression viewer’ from the BioCyc database. In addition, this tool can be used to mark all genes according to their CAI on the pathway maps.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238906&req=5

Figure 1: Outputs provided from the HEG-DB: (a) ‘Genomes consult’ shows the list of all the genomes available in the database. In this section, users can select one or more genomes to see the statistical parameters (including the codon usage correspondence analysis plot used to predict translational selection) of the selected genomes. (b) The statistical and functional information available in each gene is accessible by a global consult of a specific genome or by a search engine. This section includes the CAI value of each gene. (c) List of predicted highly expressed genes in each genome. This section includes functional and positional information about each predicted gene. (d) The metabolic pathways, which involve highly expressed genes can be viewed through the ‘pathway tools overview expression viewer’ from the BioCyc database. In addition, this tool can be used to mark all genes according to their CAI on the pathway maps.
Mentions: The information about genes and genomes is stored in a MySQL database that can be accessed through a series of PHP web pages. The current version of the database contains information about almost 200 genomes under translational selection. The HTML interface is divided into four sections (Figure 1): (i) The first section contains information about the genomes under translational selection, including links to some statistical parameters for these genomes, such as mean and standard deviations of total and positional G + C content, codon usage per thousand, relative synonymous codon usage and amino acid content. This section also includes the correspondence analysis plots of the relative synonymous codon usage for all the genes of the genomes used to predict translational selection. (ii) The second section contains the list of the predicted highly expressed genes for all of the genomes under translational selection with their functional and positional information. (iii) Since the definition of highly expressed genes is relative and depends on the limits, for each gene in the genomes under translational selection, we have included its CAI value. This information can also be accessed via a search engine that searches for gene names or keywords for a specific organism and taxa. (iv) To see the metabolic capabilities of genomes under translational selection, the fourth section enables all the genes in a genome to be represented according to their CAI value on a metabolic map, using the Pathway Tools Omics Viewer from BioCyc (22,23). The group of predicted highly expressed genes can be located separately on the metabolic pathway map of each genome. This last section makes a detailed functional analysis of the group of highly expressed genes and the preferred metabolic pathways in each genome under translational selection.Figure 1.

Bottom Line: This information can also be accessed using a search engine.Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set.The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes.

View Article: PubMed Central - PubMed

Affiliation: Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), c/Marcel-li Domingo, s/n. Campus Sescelades, 43007 Tarragona, Spain. ppuigbo@urv.cat

ABSTRACT
The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index (CAI) for all of the genes using the codon usage of the highly expressed genes as a reference set. The 'Pathway Tools Omics Viewer' from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes. The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB.

Show MeSH