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SmedGD: the Schmidtea mediterranea genome database.

Robb SM, Ross E, Sánchez Alvarado A - Nucleic Acids Res. (2007)

Bottom Line: In order to make the extensive data associated with the genome sequence accessible to the biomedical and planarian communities, we have created the Schmidtea mediterranea Genome Database (SmedGD).SmedGD integrates in a single web-accessible portal all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes.Moreover, SmedGD was designed using tools provided by the Generic Model Organism Database (GMOD) project, thus making its data structure compatible with other model organism databases.

View Article: PubMed Central - PubMed

Affiliation: Department of Neurobiology and Anatomy, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.

ABSTRACT
The planarian Schmidtea mediterranea is rapidly emerging as a model organism for the study of regeneration, tissue homeostasis and stem cell biology. The recent sequencing, assembly and annotation of its genome are expected to further buoy the biomedical importance of this organism. In order to make the extensive data associated with the genome sequence accessible to the biomedical and planarian communities, we have created the Schmidtea mediterranea Genome Database (SmedGD). SmedGD integrates in a single web-accessible portal all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes. Moreover, SmedGD was designed using tools provided by the Generic Model Organism Database (GMOD) project, thus making its data structure compatible with other model organism databases. Because of the unique phylogenetic position of planarians, SmedGD (http://smedgd.neuro.utah.edu) will prove useful not only to the planarian research community, but also to those engaged in developmental and evolutionary biology, comparative genomics, stem cell research and regeneration.

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Screen capture of SmedGD displaying genomic contig v31.019651. This contig has only one predicted gene, which has 5 exons and a 3′UTR. The tracks displayed include the gene model, its corresponding predicted transcript, and the relevant biological evidence associated with this model (see text for detailed explanations of each track). From this data, users can see the details of the gene model and its evidence (all of the predicted exons are supported by EST and protein evidence), and that the gene is likely coding for a histone deacetylase. Double-stranded RNA has been used to silence this gene and the resulting phenotypes are listed. cDNA Microarray data is not yet available, but a sample of how this information will be viewed is presented. An arrow pointing down indicates down-regulation of the gene in the experimental group.
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Figure 1: Screen capture of SmedGD displaying genomic contig v31.019651. This contig has only one predicted gene, which has 5 exons and a 3′UTR. The tracks displayed include the gene model, its corresponding predicted transcript, and the relevant biological evidence associated with this model (see text for detailed explanations of each track). From this data, users can see the details of the gene model and its evidence (all of the predicted exons are supported by EST and protein evidence), and that the gene is likely coding for a histone deacetylase. Double-stranded RNA has been used to silence this gene and the resulting phenotypes are listed. cDNA Microarray data is not yet available, but a sample of how this information will be viewed is presented. An arrow pointing down indicates down-regulation of the gene in the experimental group.

Mentions: We made sure that the mySQL database generated from the GFF3 files conformed to GMOD standards. Therefore, we parsed the database using GBrowse, which implemented a Bio::DB::SeqFeature::Store database adaptor to access and display rows of data or tracks that are mapped to specific locations in the genome (Figure 1). Customizations to the standard GMOD distribution were also made to accommodate additional database searching and sequence retrieval. CGI scripts that interface with SmedGD's mySQL database using DBI, a perl module, enable specialized queries of GO terms and RNAi phenotypes, and uniquely formatted protein homology search results. Changes made to the GBrowse configuration file allow for the linking to a CGI script that uses ‘fastacmd’, free software distributed by the NCBI (http://www.ncbi.nlm.nih.gov), to retrieve sequences from specially formatted fasta files and displays them when the ‘Name’ of an mRNA is selected in the mRNA ‘Details Page’ (see below). The web page displaying the retrieved sequence includes a link to the NCBI BLAST web server, which when selected will auto fill the NCBI BLAST forms with the retrieved planarian sequence.Figure 1.


SmedGD: the Schmidtea mediterranea genome database.

Robb SM, Ross E, Sánchez Alvarado A - Nucleic Acids Res. (2007)

Screen capture of SmedGD displaying genomic contig v31.019651. This contig has only one predicted gene, which has 5 exons and a 3′UTR. The tracks displayed include the gene model, its corresponding predicted transcript, and the relevant biological evidence associated with this model (see text for detailed explanations of each track). From this data, users can see the details of the gene model and its evidence (all of the predicted exons are supported by EST and protein evidence), and that the gene is likely coding for a histone deacetylase. Double-stranded RNA has been used to silence this gene and the resulting phenotypes are listed. cDNA Microarray data is not yet available, but a sample of how this information will be viewed is presented. An arrow pointing down indicates down-regulation of the gene in the experimental group.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238899&req=5

Figure 1: Screen capture of SmedGD displaying genomic contig v31.019651. This contig has only one predicted gene, which has 5 exons and a 3′UTR. The tracks displayed include the gene model, its corresponding predicted transcript, and the relevant biological evidence associated with this model (see text for detailed explanations of each track). From this data, users can see the details of the gene model and its evidence (all of the predicted exons are supported by EST and protein evidence), and that the gene is likely coding for a histone deacetylase. Double-stranded RNA has been used to silence this gene and the resulting phenotypes are listed. cDNA Microarray data is not yet available, but a sample of how this information will be viewed is presented. An arrow pointing down indicates down-regulation of the gene in the experimental group.
Mentions: We made sure that the mySQL database generated from the GFF3 files conformed to GMOD standards. Therefore, we parsed the database using GBrowse, which implemented a Bio::DB::SeqFeature::Store database adaptor to access and display rows of data or tracks that are mapped to specific locations in the genome (Figure 1). Customizations to the standard GMOD distribution were also made to accommodate additional database searching and sequence retrieval. CGI scripts that interface with SmedGD's mySQL database using DBI, a perl module, enable specialized queries of GO terms and RNAi phenotypes, and uniquely formatted protein homology search results. Changes made to the GBrowse configuration file allow for the linking to a CGI script that uses ‘fastacmd’, free software distributed by the NCBI (http://www.ncbi.nlm.nih.gov), to retrieve sequences from specially formatted fasta files and displays them when the ‘Name’ of an mRNA is selected in the mRNA ‘Details Page’ (see below). The web page displaying the retrieved sequence includes a link to the NCBI BLAST web server, which when selected will auto fill the NCBI BLAST forms with the retrieved planarian sequence.Figure 1.

Bottom Line: In order to make the extensive data associated with the genome sequence accessible to the biomedical and planarian communities, we have created the Schmidtea mediterranea Genome Database (SmedGD).SmedGD integrates in a single web-accessible portal all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes.Moreover, SmedGD was designed using tools provided by the Generic Model Organism Database (GMOD) project, thus making its data structure compatible with other model organism databases.

View Article: PubMed Central - PubMed

Affiliation: Department of Neurobiology and Anatomy, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.

ABSTRACT
The planarian Schmidtea mediterranea is rapidly emerging as a model organism for the study of regeneration, tissue homeostasis and stem cell biology. The recent sequencing, assembly and annotation of its genome are expected to further buoy the biomedical importance of this organism. In order to make the extensive data associated with the genome sequence accessible to the biomedical and planarian communities, we have created the Schmidtea mediterranea Genome Database (SmedGD). SmedGD integrates in a single web-accessible portal all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes. Moreover, SmedGD was designed using tools provided by the Generic Model Organism Database (GMOD) project, thus making its data structure compatible with other model organism databases. Because of the unique phylogenetic position of planarians, SmedGD (http://smedgd.neuro.utah.edu) will prove useful not only to the planarian research community, but also to those engaged in developmental and evolutionary biology, comparative genomics, stem cell research and regeneration.

Show MeSH
Related in: MedlinePlus