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Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

Sullivan JC, Reitzel AM, Finnerty JR - Nucleic Acids Res. (2007)

Bottom Line: The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics.StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community.Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Boston University, Boston, MA 02215, USA.

ABSTRACT
The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.

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Pipeline for the development of (A) StellaBase Disease and (B) StellaBase SNP.
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Figure 2: Pipeline for the development of (A) StellaBase Disease and (B) StellaBase SNP.

Mentions: To develop StellaBase Disease, we downloaded the OMIM database and select tables from GenBank (Genbank tables: gene2accession and mim2gene;Figure 2a, Step ‘A’). Cross-referencing between genemap, mim2gene and gene2accession allowed for the identification and downloading of all alleles associated with the 10 237 OMIM entries available on 15 July 2007 (Figure 2a, Steps ‘B’ and ‘C’). The protein datasets for fly, nematode and baker's yeast were downloaded from NCBI (Figure 2a, Step ‘D’). These datasets, and the predicted proteins available in StellaBase v.1.0, were formatted as blast databases and were searched with the retrieved human disease allele database using BLASTP (10). The resultant BLASTP output and OMIM data are stored in a relational database cross-referenced with the main structure of StellaBase (Figure 3).Figure 2.


Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

Sullivan JC, Reitzel AM, Finnerty JR - Nucleic Acids Res. (2007)

Pipeline for the development of (A) StellaBase Disease and (B) StellaBase SNP.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238866&req=5

Figure 2: Pipeline for the development of (A) StellaBase Disease and (B) StellaBase SNP.
Mentions: To develop StellaBase Disease, we downloaded the OMIM database and select tables from GenBank (Genbank tables: gene2accession and mim2gene;Figure 2a, Step ‘A’). Cross-referencing between genemap, mim2gene and gene2accession allowed for the identification and downloading of all alleles associated with the 10 237 OMIM entries available on 15 July 2007 (Figure 2a, Steps ‘B’ and ‘C’). The protein datasets for fly, nematode and baker's yeast were downloaded from NCBI (Figure 2a, Step ‘D’). These datasets, and the predicted proteins available in StellaBase v.1.0, were formatted as blast databases and were searched with the retrieved human disease allele database using BLASTP (10). The resultant BLASTP output and OMIM data are stored in a relational database cross-referenced with the main structure of StellaBase (Figure 3).Figure 2.

Bottom Line: The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics.StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community.Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Boston University, Boston, MA 02215, USA.

ABSTRACT
The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.

Show MeSH