Limits...
ProSAS: a database for analyzing alternative splicing in the context of protein structures.

Birzele F, Küffner R, Meier F, Oefinger F, Potthast C, Zimmer R - Nucleic Acids Res. (2007)

Bottom Line: Nevertheless, the effects of splicing on the structure of a protein are largely unknown.The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures.ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events.

View Article: PubMed Central - PubMed

Affiliation: Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstrasse 17, D-80333 Munich, Germany.

ABSTRACT
Alternative splicing is known to be one of the major sources for functional diversity in higher eukaryotes. Several splicing isoforms have been characterized in the literature that play important roles in cellular processes like apoptosis or signal transduction pathways. Splicing events can often be detected on the mRNA level by large-scale cDNA or EST experiments and such data is collected and annotated in several databases. Nevertheless, the effects of splicing on the structure of a protein are largely unknown. The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures. ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events. Alternative isoforms annotated in Ensembl or SwissProt can be analyzed on the protein structure and protein function level using an intuitive user interface that provides several features and tools for a structure-based analysis of alternative splicing events. The ProSAS database is freely accessible at http://www.bio.ifi.lmu.de/ProSAS.

Show MeSH
Database content and annotation pipeline. Gene and alternative transcript information is obtained from the Ensembl database as well as from SwissProt. Additional information comes from InterPro patterns and orthologs are mapped by Ensembl database using BioMart. Protein structures from the PDB are annotated to transcripts using SIMAP and several structural features are computed using SCOP, PDP and DSSP annotations. Other data like the (structural) variance in the corresponding protein family will be added in the future (Other methods). Affymetrix probesets are mapped onto transcripts and genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238869&req=5

Figure 1: Database content and annotation pipeline. Gene and alternative transcript information is obtained from the Ensembl database as well as from SwissProt. Additional information comes from InterPro patterns and orthologs are mapped by Ensembl database using BioMart. Protein structures from the PDB are annotated to transcripts using SIMAP and several structural features are computed using SCOP, PDP and DSSP annotations. Other data like the (structural) variance in the corresponding protein family will be added in the future (Other methods). Affymetrix probesets are mapped onto transcripts and genes.

Mentions: Figure 1 shows an overview on the database content and the annotation pipeline used in the ProSAS database, while Table 1 summarizes the current content of the database.Figure 1.


ProSAS: a database for analyzing alternative splicing in the context of protein structures.

Birzele F, Küffner R, Meier F, Oefinger F, Potthast C, Zimmer R - Nucleic Acids Res. (2007)

Database content and annotation pipeline. Gene and alternative transcript information is obtained from the Ensembl database as well as from SwissProt. Additional information comes from InterPro patterns and orthologs are mapped by Ensembl database using BioMart. Protein structures from the PDB are annotated to transcripts using SIMAP and several structural features are computed using SCOP, PDP and DSSP annotations. Other data like the (structural) variance in the corresponding protein family will be added in the future (Other methods). Affymetrix probesets are mapped onto transcripts and genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238869&req=5

Figure 1: Database content and annotation pipeline. Gene and alternative transcript information is obtained from the Ensembl database as well as from SwissProt. Additional information comes from InterPro patterns and orthologs are mapped by Ensembl database using BioMart. Protein structures from the PDB are annotated to transcripts using SIMAP and several structural features are computed using SCOP, PDP and DSSP annotations. Other data like the (structural) variance in the corresponding protein family will be added in the future (Other methods). Affymetrix probesets are mapped onto transcripts and genes.
Mentions: Figure 1 shows an overview on the database content and the annotation pipeline used in the ProSAS database, while Table 1 summarizes the current content of the database.Figure 1.

Bottom Line: Nevertheless, the effects of splicing on the structure of a protein are largely unknown.The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures.ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events.

View Article: PubMed Central - PubMed

Affiliation: Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstrasse 17, D-80333 Munich, Germany.

ABSTRACT
Alternative splicing is known to be one of the major sources for functional diversity in higher eukaryotes. Several splicing isoforms have been characterized in the literature that play important roles in cellular processes like apoptosis or signal transduction pathways. Splicing events can often be detected on the mRNA level by large-scale cDNA or EST experiments and such data is collected and annotated in several databases. Nevertheless, the effects of splicing on the structure of a protein are largely unknown. The ProSAS (Protein Structure and Alternative Splicing) database fills this gap and provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures. ProSAS comprehensively annotates and models protein structures for several Ensembl genomes as well as SwissProt entries harbouring splicing events. Alternative isoforms annotated in Ensembl or SwissProt can be analyzed on the protein structure and protein function level using an intuitive user interface that provides several features and tools for a structure-based analysis of alternative splicing events. The ProSAS database is freely accessible at http://www.bio.ifi.lmu.de/ProSAS.

Show MeSH