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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.

Show MeSH
Number of families (A), average size of families (B), ratio of paralogs (C) and number of paralogons (D) in different genomes. Number of genes denotes the size of a genome, r is the correlation coefficient and P is P-value.
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Figure 3: Number of families (A), average size of families (B), ratio of paralogs (C) and number of paralogons (D) in different genomes. Number of genes denotes the size of a genome, r is the correlation coefficient and P is P-value.

Mentions: Consistent with previous studies on Bacteria and a small set of Eukarya (9,29,31), large genomes possess more paralog families and a higher proportion of genes belonging to paralog families than small genomes (Figure 3A and C). We find, however, only a weak correlation between the average size of families and the genome sizes (Figure 3B, r = 0.26, P = 0.19), in contrast to the finding in Bacteria that average family size increases with genome size (31). This result suggests that the higher percentage of paralogs in large eukaryotic genome stems mainly from the emergence of new paralogon families. An expansion of existing gene families is not evident in Eukarya (Figure 3B).Figure 3.


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)

Number of families (A), average size of families (B), ratio of paralogs (C) and number of paralogons (D) in different genomes. Number of genes denotes the size of a genome, r is the correlation coefficient and P is P-value.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Number of families (A), average size of families (B), ratio of paralogs (C) and number of paralogons (D) in different genomes. Number of genes denotes the size of a genome, r is the correlation coefficient and P is P-value.
Mentions: Consistent with previous studies on Bacteria and a small set of Eukarya (9,29,31), large genomes possess more paralog families and a higher proportion of genes belonging to paralog families than small genomes (Figure 3A and C). We find, however, only a weak correlation between the average size of families and the genome sizes (Figure 3B, r = 0.26, P = 0.19), in contrast to the finding in Bacteria that average family size increases with genome size (31). This result suggests that the higher percentage of paralogs in large eukaryotic genome stems mainly from the emergence of new paralogon families. An expansion of existing gene families is not evident in Eukarya (Figure 3B).Figure 3.

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