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Rapid Approach for Seed optimization Based on a Hill-climbing Algorithm that is Repeated Iteratively rasbhari

Online

Calculates sets of binary patterns for read mapping, database searching and alignment-free sequence comparison. For sequence-homology searching, Rasbhari optimizes the sensitivity of pattern sets. Since the sensitivity of a pattern set is expensive to calculate, the algorithm optimizes the overlap complexity of the produced pattern sets which is closely related to its sensitivity.

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rasbhari versioning

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rasbhari classification

rasbhari specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++
Version:
1.3.0
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

rasbhari support

Maintainer

  • Lars Hahn <>

Credits

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Publications

Institution(s)

Department of Bioinformatics, University of Göttingen, Göttingen, Germany; Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Center for Computational Sciences, University of Göttingen, Göttingen, Germany

Funding source(s)

This work was funded by the budget of the Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, by the budget of the Department of Computer Science and Engineering, University of California, Riverside, USA and by the graduate student support NSF IIS- 1526742 and NSF IIS-1302134.

Link to literature

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