The ProSAS Database

• 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.

Enter ProSAS: HERE (please check the following requirements first!)

Requirements

The ProSAS web interface has the following requirements on your browser and your system:

• Tested Browsers: The following internet browsers have been tested successfully with ProSAS: Mozilla Firefox (versions 1.5 and 2.0) on Linux, Windows and MacOS, Internet Explorer (versions 5 and 6). We recommend to use Firefox, which can be for example downloaded here. ProSAS has known problems with Konqueror under Linux and with Safari Apple MacOS.
• JavaScript must be activated: The interactive web interface of ProSAS requires JavaScript to be activated in your browser. This can be done in the following way:
  • 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.
  • Netscape Navigator (4.8): Select 'Edit' from the top menu, choose 'Preferences', choose 'Advanced', choose 'Scripts & Plugins', select the 'Enable JavaScript' checkbox and click OK
  • Mozilla Firefox (1.0): Select 'Tools' from the top menu, choose 'Options', choose 'Web Features' from the left navigation, select the checkbox next to 'Enable JavaScript' and click OK
  • Mozilla Firefox (1.5 and 2.0): Select 'Tools' from the top menu, choose 'Options', choose 'Content' from the top navigation, select the checkbox next to 'Enable JavaScript' 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 me.

• 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.

• How to search the ProSAS database
• How to access detailed information about genes in the ProSAS database
• How to access detailed information about transcripts in the ProSAS database
• How to access detailed information about Swissprot entries in the ProSAS database
• How to access information about orthologous genes for human in mouse and rat
• ProSAS flat file export format 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

• Genome data
• Affy Data
• Structure Data
• Swissprot Data
• Additional Data

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

ProSAS is implemented using Zkoss.