ProSAS (Protein Structure and Alternative Splicing) database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database which provides several features and tools which are described shortly in detail in this tutorial.
14.07.2008:: Novel ProSAS database online including the Chimpanzee genome, novel structure and Interpro predictions... Also several improvements within the user interface.
04.03.2008:: ProSAS tutorial has been rewritten and ProSAS now provides context information. The results of our exon chip analysis pipeline for human may now be accessed very conveniently for every gene.
22.10.2007: ProSAS is now connected to our exon chip analysis pipeline. To date, ProSAS displays expression levels for genes and exons in 11 different tissues (the Affymetrix example chips) for Human, Mouse and Rat and more analysis features are soon to come.
19.10.2007: ProSAS now allows users to directly export data from the database as flat text files! Additionally, ProSAS now uses the most recent Zkoss 3.0 framework which is more stable and faster than previous versions.
(please check the following requirements first!)
The ProSAS web interface has the following requirements on your browser and your system:
Internet Explorer (6.0): Select 'Tools' from the top menu, choose 'Internet Options', click on the 'Security' tab, click on 'Custom Level', scroll down until you see section labled 'Scripting', under 'Active Scripting', select 'Enable' and click OK.
Java must be installed: In order to use the full ProSAS functionality, Java needs to be installed on your system since it is required to run Jmol which is used to visualize protein structures. You can check your Java installation by following this link. If Java is not available on your system it needs to be installed. To do so, follow this link and the instructions given on this site.
If you observe any problems with other browsers or if you have problems in running ProSAS please contact
Make sure that
Java is installed and Java Script is activated. This may solve most problems ;-) If the
Jmol plugin is not able to load structure (after you have successfully loaded several structures before) please close your internet browser and restart the database. In that case, the memory assigned to the virtual machine is full and no more structures can be loaded.
Database Download and Documentation
Here you can download the ProSAS database as MySQL dumps which can be used to prot the database to virtually any SQL database system. If you have any questions regarding the database please feel free to contact me at
fabian.birzele * at * bio.ifi.lmu.de
External Data Sources
ProSAS makes use of knowledge stored in several external databases and combines those resources and additional information computed in house to an informative resource for analyzing alternative splicing in the context of protein structure. In particular, the following databases and services are used
Ensembl: basic resource for all genome data for human, mouse and rat as well as annotated splicing events for those genomes.
Swissprot: additional resource for alternative splicing events and protein data.
SIMAP: SIMAP is used for several applications including the search for homologous proteins in the PDB as well as the Interpro pattern annotation provided by the database. Special thanks to Thomas Rattei for providing this information.
Biomart: some additional data (GO annotations, Ensembl annotated orthologs, Ensembl Gene annotations) is obtained from the Biomart service
PDB: protein structure data is obtained from the PDB database
is implemented using