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SIMAP - Similarity Matrix of Proteins


  11:57:36 am, by The Dreamer   , 372 words  
Categories: BOINC

SIMAP - Similarity Matrix of Proteins

Link: http://boinc.bio.wzw.tum.de/boincsimap/


What is SIMAP?
SIMAP is a database of protein similarities. It contains about all currently published protein sequences and is continuously updated. Protein similarities are computed using the FASTA algorithm which provides optimal speed and sensitivity. SIMAP is to our knowledge the only project that combines comprehensive coverage with respect to all known proteins and incremental update capabilities.

What is SIMAP used for?
Because of the huge amount of known protein sequences in public databases it became clear that most of them will not be experimentally characterized in the near future. Nevertheless, proteins that have evolved from a common ancestor often share same functions (so-called orthologs). So it is possible to infer the function of a non-characterized protein from an ortholog with known function. A well-known example are the investigations about mouse genes and proteins. Their results are also beeing true for orthologous human genes and proteins in many cases. Protein similarities provide information about relations between proteins and are necessary for the prediction of orthologs. There are many more bioinformatics methods that rely on protein similarity. Our protein similarity database provides pre-computed similarity data and represents the known protein space. This opens completely new perspectives compared to the commonly used method to repeatedly re-calculate such kind of data. SIMAP is regularly updated. The similarity matrix is simply beeing incrementally extended if new sequences occur. The use of SIMAP is completely free for education and public research.

Why do we need distributed computing for SIMAP?
The computational costs to calculate the similarity data depend on the square of the number of contained sequences. So the computational effort for keeping the matrix up-to-date is constantly increasing. Our internal resources that perform calculations for SIMAP since years are not longer sufficient to keep track of all new sequences. That's why we implemented a SIMAP-client for the BOINC platform (Berkeley Open Infrastructure for Network Computing) which is based on the FASTA algorithm to detect sequence similarities.

What are the institutions behind SIMAP?
SIMAP is a joint project of the GSF National Research Center for Environment and Health, Neuherberg and Technical University Munich, Center of Life and Food Science Weihenstephan (both in Germany). Please contact Thomas Rattei (Department of Genome Oriented Bioinformatics, TU Munich).

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