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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
Database searching. (A) Quick search for ‘any text’ or sequences. (B) Advanced text search. NCBI Gene ID, member ID, paralog family ID, paralogon ID, gene symbol and any word in the gene description can be applied as search fields. (C) Advanced sequence search by NCBI BLAST (20). (D) Query result with a navigation bar.
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Figure 2: Database searching. (A) Quick search for ‘any text’ or sequences. (B) Advanced text search. NCBI Gene ID, member ID, paralog family ID, paralogon ID, gene symbol and any word in the gene description can be applied as search fields. (C) Advanced sequence search by NCBI BLAST (20). (D) Query result with a navigation bar.

Mentions: The user can access the records in the EPGD with customized queries (Figure 2). From the ‘iSearch’ webpage (Figure 2A), ‘any text’ and nucleic acid or protein sequences can be searched without setting any parameter. Advanced Search pages with numerous input options (Figure 2B and C) can be accessed via the links (‘Advanced Text Search’ or ‘Advanced Sequence Search’) from ‘iSearch’ page. The sequence search is powered by NCBI Blast package (20). Each search returns a result list of records in the database, which provides the hyperlinks to detailed pages (Figure 2D).Figure 2.


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)

Database searching. (A) Quick search for ‘any text’ or sequences. (B) Advanced text search. NCBI Gene ID, member ID, paralog family ID, paralogon ID, gene symbol and any word in the gene description can be applied as search fields. (C) Advanced sequence search by NCBI BLAST (20). (D) Query result with a navigation bar.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Database searching. (A) Quick search for ‘any text’ or sequences. (B) Advanced text search. NCBI Gene ID, member ID, paralog family ID, paralogon ID, gene symbol and any word in the gene description can be applied as search fields. (C) Advanced sequence search by NCBI BLAST (20). (D) Query result with a navigation bar.
Mentions: The user can access the records in the EPGD with customized queries (Figure 2). From the ‘iSearch’ webpage (Figure 2A), ‘any text’ and nucleic acid or protein sequences can be searched without setting any parameter. Advanced Search pages with numerous input options (Figure 2B and C) can be accessed via the links (‘Advanced Text Search’ or ‘Advanced Sequence Search’) from ‘iSearch’ page. The sequence search is powered by NCBI Blast package (20). Each search returns a result list of records in the database, which provides the hyperlinks to detailed pages (Figure 2D).Figure 2.

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