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GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D - Nucleic Acids Res. (2007)

Bottom Line: Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable.The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information.GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164-6414, USA. sook@bioinfo.wsu.edu

ABSTRACT
The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

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Related in: MedlinePlus

EST and contig page. (A) SSR/ORF information page showing the EST sequence along with the position of SSRs and the longest ORF. (B) Unigene information page showing the assembly displaying the unigene resulted from genus or family level assembly. The unigene name is linked to the corresponding contig page. (C) Contig information page with the sequence and the side bar. (D) Contig sequence homology page showing the best SWISS-PROT and TrEMBL matches.
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Figure 1: EST and contig page. (A) SSR/ORF information page showing the EST sequence along with the position of SSRs and the longest ORF. (B) Unigene information page showing the assembly displaying the unigene resulted from genus or family level assembly. The unigene name is linked to the corresponding contig page. (C) Contig information page with the sequence and the side bar. (D) Contig sequence homology page showing the best SWISS-PROT and TrEMBL matches.

Mentions: Instead of displaying all the details on one page, the EST details page initially displays the clone information and the sequence with a side bar containing links to library details, unigene information, sequence homology, SSR/ORF information, map position and anchored BACs when applicable (Figure 1). A unigene information page provides the contig name and hyperlink for both the genus and family unigenes (Figure 1). The contig page gives similar annotation data for the contig with additional links to the SNP results and the comprising ESTs. Also available from the EST or contig page is the InterProScan Web Services. This Web Service allows users to directly scan for protein signatures without going to the EBI site and uploading the sequences. For the ESTs anchored to peach BACs and/or to Rosaceae genetic maps, the EST detail page provides a link to view the ESTs' map positions using the GDR Map Viewer or CMap.Figure 1.


GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D - Nucleic Acids Res. (2007)

EST and contig page. (A) SSR/ORF information page showing the EST sequence along with the position of SSRs and the longest ORF. (B) Unigene information page showing the assembly displaying the unigene resulted from genus or family level assembly. The unigene name is linked to the corresponding contig page. (C) Contig information page with the sequence and the side bar. (D) Contig sequence homology page showing the best SWISS-PROT and TrEMBL matches.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238863&req=5

Figure 1: EST and contig page. (A) SSR/ORF information page showing the EST sequence along with the position of SSRs and the longest ORF. (B) Unigene information page showing the assembly displaying the unigene resulted from genus or family level assembly. The unigene name is linked to the corresponding contig page. (C) Contig information page with the sequence and the side bar. (D) Contig sequence homology page showing the best SWISS-PROT and TrEMBL matches.
Mentions: Instead of displaying all the details on one page, the EST details page initially displays the clone information and the sequence with a side bar containing links to library details, unigene information, sequence homology, SSR/ORF information, map position and anchored BACs when applicable (Figure 1). A unigene information page provides the contig name and hyperlink for both the genus and family unigenes (Figure 1). The contig page gives similar annotation data for the contig with additional links to the SNP results and the comprising ESTs. Also available from the EST or contig page is the InterProScan Web Services. This Web Service allows users to directly scan for protein signatures without going to the EBI site and uploading the sequences. For the ESTs anchored to peach BACs and/or to Rosaceae genetic maps, the EST detail page provides a link to view the ESTs' map positions using the GDR Map Viewer or CMap.Figure 1.

Bottom Line: Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable.The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information.GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools.

View Article: PubMed Central - PubMed

Affiliation: Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164-6414, USA. sook@bioinfo.wsu.edu

ABSTRACT
The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

Show MeSH
Related in: MedlinePlus