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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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Related in: MedlinePlus

(A) The ‘Protein Homology’ Search interface. In this example, the search term ‘piwi-like’ is being submitted. Each of the hits from SwissProt, SMART, PFAM and the species-specific databases are searched for the user query term. (B) Results of the search are sorted by genomic contig and location. When more than one result is found on one contig, the matches are grouped and the background will be similarly colored. When there is more than one protein match for one genomic location, it is often due to this sequence matching more than one database. When there is only one result per contig the background is colored white. The contig and location are hyperlinked to the genome browser for further inspection.
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Figure 2: (A) The ‘Protein Homology’ Search interface. In this example, the search term ‘piwi-like’ is being submitted. Each of the hits from SwissProt, SMART, PFAM and the species-specific databases are searched for the user query term. (B) Results of the search are sorted by genomic contig and location. When more than one result is found on one contig, the matches are grouped and the background will be similarly colored. When there is more than one protein match for one genomic location, it is often due to this sequence matching more than one database. When there is only one result per contig the background is colored white. The contig and location are hyperlinked to the genome browser for further inspection.

Mentions: The Search tools provide methods for users to directly query the databases of SmedGD. Sequences can be used to find homologs in S. mediterranea by using BLAST and BLAT. Both nucleotide and protein sequences can be used with BLAST, while BLAT will search the whole genome with nucleotide sequences only. The BLAT result page contains a button that will link the results to an auto-generated track in the browser, such that the queried sequence will be aligned visually to the genome and will be in correct alignment with the other data tracks. In the Search page a user can query the text data stored in SmedGD. Protein homology is queried in the Swissprot, SMART, PFAM and proteome hits to the genome (Figure 2A and B). Gene Ontology terms can be searched by cellular location, molecular function or biological process (Figure 3A). Finally RNAi phenotypes can also be queried with an assortment of checkboxes and drop down menus in an additive ‘AND’ fashion (Figure 3B).Figure 2.


SmedGD: the Schmidtea mediterranea genome database.

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

(A) The ‘Protein Homology’ Search interface. In this example, the search term ‘piwi-like’ is being submitted. Each of the hits from SwissProt, SMART, PFAM and the species-specific databases are searched for the user query term. (B) Results of the search are sorted by genomic contig and location. When more than one result is found on one contig, the matches are grouped and the background will be similarly colored. When there is more than one protein match for one genomic location, it is often due to this sequence matching more than one database. When there is only one result per contig the background is colored white. The contig and location are hyperlinked to the genome browser for further inspection.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: (A) The ‘Protein Homology’ Search interface. In this example, the search term ‘piwi-like’ is being submitted. Each of the hits from SwissProt, SMART, PFAM and the species-specific databases are searched for the user query term. (B) Results of the search are sorted by genomic contig and location. When more than one result is found on one contig, the matches are grouped and the background will be similarly colored. When there is more than one protein match for one genomic location, it is often due to this sequence matching more than one database. When there is only one result per contig the background is colored white. The contig and location are hyperlinked to the genome browser for further inspection.
Mentions: The Search tools provide methods for users to directly query the databases of SmedGD. Sequences can be used to find homologs in S. mediterranea by using BLAST and BLAT. Both nucleotide and protein sequences can be used with BLAST, while BLAT will search the whole genome with nucleotide sequences only. The BLAT result page contains a button that will link the results to an auto-generated track in the browser, such that the queried sequence will be aligned visually to the genome and will be in correct alignment with the other data tracks. In the Search page a user can query the text data stored in SmedGD. Protein homology is queried in the Swissprot, SMART, PFAM and proteome hits to the genome (Figure 2A and B). Gene Ontology terms can be searched by cellular location, molecular function or biological process (Figure 3A). Finally RNAi phenotypes can also be queried with an assortment of checkboxes and drop down menus in an additive ‘AND’ fashion (Figure 3B).Figure 2.

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