SIMAP
| SIMAP @ home | |
|---|---|
| Area: | biochemistry |
| Target: | Calculation of the similarity of protein sequences and storage in a database |
| Operator: | University of Vienna |
| Country: | Germany |
| Platform: | BOINC |
| Website: | boincsimap.org/boincsimap |
| Project status | |
| Status: | completed |
| Start: | 12/13/2005 |
| The End: | December 31, 2014 |
SIMAP ( Si milarity Ma trix of P roteins ; dt .: similarity matrix for proteins ) is a database for protein similarities. This database contains all previously published protein sequences and is continuously updated. Similarities of the proteins are calculated using the FASTA algorithm . It is the only such database to date that actually includes all previously known proteins. A new SIMAP database (SIMAP2) has been developed since 2014. SIMAP2 uses the exact Smith-Waterman algorithm and should therefore achieve better sensitivity than the original project. This was last updated at the end of 2014, but will remain online as long as it is scientifically relevant. SIMAP2 is no longer calculated with BOINCSIMAP, but with a high-performance computer from the University of Vienna .
background
Protein similarities are an important tool in bioinformatics . They provide a measure of some kind of relationship between different proteins. Since the number of known proteins by far exceeds the amount that can be examined experimentally in laboratories, the properties of proteins that have already been examined are transferred to close relatives, i.e. very similar proteins. So far, these similarities have been calculated over and over again as required. With SIMAP, these similarities are now fully calculated in advance and stored in the database, not when required. SIMAP is a joint project of the GSF Research Center for Health and Environment in Neuherberg and the Technical University of Munich and is completely free of charge for research and teaching.
BOINCSIMAP
Since the immensely high computational effort in the prediction of the similarities SIMAP exceeds -Capacities, the decision was made with the project BOINCSIMAP and the program SIMAP @ home on means of distributed computing to access. For this purpose, a client was developed on the basis of FASTA , which uses the BOINC infrastructure.
Another program called HMMER uses the Hidden Markov Model to search for protein domains and is also occasionally used with BOINCSIMAP.
Data from the PDB , RefSeq , UniProt and GenBank databases are used to analyze the sequence similarities and domains .
In February 2014, Samsung Austria started offering an app for the Android operating system under the name PowerSleep , which offers the possibility of making the computing power of a smartphone available for this research project during the night. The app basically also works on non-Samsung smartphones.
See also
Web links
Individual evidence
- ↑ HMMER (English) - official project website; As of December 23, 2007
- ↑ BOINCSIMAP News ( Memento of the original dated December 30, 2010 in the Internet Archive ) Info: The archive link was automatically inserted and not yet checked. Please check the original and archive link according to the instructions and then remove this notice. - Report to BOINCSIMAP ; Status: October 12, 2007
- ↑ Samsung's PowerSleep website, accessed February 20, 2014
