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EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Ding G, Sun Y, Li H, Wang Z, Fan H, Wang C, Yang D, Li Y - Nucleic Acids Res. (2007)

Bottom Line: Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons).The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files.The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, P. R. China.

ABSTRACT
Gene duplication is common in all three domains of life, especially in eukaryotic genomes. The duplicates provide new material for the action of evolutionary forces such as selection or genetic drift. Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons). We also constructed an internet-accessible Eukaryotic Paralog Group Database (EPGD; http://epgd.biosino.org/EPGD/). The database is gene-centered and organized by paralog family. It focuses on paralogs and evolutionary duplication events. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files. The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families.

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Web pages for gene record (A), paralog family (B) and paralogon region (C). (A) Example of a gene record for H. sapiens. The gene record web page consists of three segments: basic information, paralogon links and coding sequences. Through paralogon links, paralogons ‘including’ or ‘covering’ this gene can be accessed. (B) Example of a paralog family. Gene list, multi-alignment and pre-calculated evolutionary indexes can be obtained from this page. The user can visualize the multi-alignment via JalView (28). In addition, an UPGMA tree is built and rendered with a Java applet. (C) Paralogon region with a highlighted gene (colored red). Several basic properties (average block length, average block density, number of links) are displayed in the page. In the paralogon figures, the paralogs in these regions are connected with lines. Each gene in these figures is linked to the gene record in database.
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Figure 1: Web pages for gene record (A), paralog family (B) and paralogon region (C). (A) Example of a gene record for H. sapiens. The gene record web page consists of three segments: basic information, paralogon links and coding sequences. Through paralogon links, paralogons ‘including’ or ‘covering’ this gene can be accessed. (B) Example of a paralog family. Gene list, multi-alignment and pre-calculated evolutionary indexes can be obtained from this page. The user can visualize the multi-alignment via JalView (28). In addition, an UPGMA tree is built and rendered with a Java applet. (C) Paralogon region with a highlighted gene (colored red). Several basic properties (average block length, average block density, number of links) are displayed in the page. In the paralogon figures, the paralogs in these regions are connected with lines. Each gene in these figures is linked to the gene record in database.

Mentions: The web interface was implemented using Java and JavaServer Pages technologies. The user can inspect the datasets in the EPGD and see a summary of the current version. The records of paralog families, paralogons and genes (Figure 1) are randomly selected each time when ‘Glance’ page is visited (http://epgd.biosino.org/EPGD/glance.jsp).Figure 1.


EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Ding G, Sun Y, Li H, Wang Z, Fan H, Wang C, Yang D, Li Y - Nucleic Acids Res. (2007)

Web pages for gene record (A), paralog family (B) and paralogon region (C). (A) Example of a gene record for H. sapiens. The gene record web page consists of three segments: basic information, paralogon links and coding sequences. Through paralogon links, paralogons ‘including’ or ‘covering’ this gene can be accessed. (B) Example of a paralog family. Gene list, multi-alignment and pre-calculated evolutionary indexes can be obtained from this page. The user can visualize the multi-alignment via JalView (28). In addition, an UPGMA tree is built and rendered with a Java applet. (C) Paralogon region with a highlighted gene (colored red). Several basic properties (average block length, average block density, number of links) are displayed in the page. In the paralogon figures, the paralogs in these regions are connected with lines. Each gene in these figures is linked to the gene record in database.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238967&req=5

Figure 1: Web pages for gene record (A), paralog family (B) and paralogon region (C). (A) Example of a gene record for H. sapiens. The gene record web page consists of three segments: basic information, paralogon links and coding sequences. Through paralogon links, paralogons ‘including’ or ‘covering’ this gene can be accessed. (B) Example of a paralog family. Gene list, multi-alignment and pre-calculated evolutionary indexes can be obtained from this page. The user can visualize the multi-alignment via JalView (28). In addition, an UPGMA tree is built and rendered with a Java applet. (C) Paralogon region with a highlighted gene (colored red). Several basic properties (average block length, average block density, number of links) are displayed in the page. In the paralogon figures, the paralogs in these regions are connected with lines. Each gene in these figures is linked to the gene record in database.
Mentions: The web interface was implemented using Java and JavaServer Pages technologies. The user can inspect the datasets in the EPGD and see a summary of the current version. The records of paralog families, paralogons and genes (Figure 1) are randomly selected each time when ‘Glance’ page is visited (http://epgd.biosino.org/EPGD/glance.jsp).Figure 1.

Bottom Line: Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons).The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files.The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, P. R. China.

ABSTRACT
Gene duplication is common in all three domains of life, especially in eukaryotic genomes. The duplicates provide new material for the action of evolutionary forces such as selection or genetic drift. Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons). We also constructed an internet-accessible Eukaryotic Paralog Group Database (EPGD; http://epgd.biosino.org/EPGD/). The database is gene-centered and organized by paralog family. It focuses on paralogs and evolutionary duplication events. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files. The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families.

Show MeSH