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Context-specific mutation probabilities for protein sequencing searching.
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Dependencies ----------------- CS-BLAST requires the 'sparsehash' library, which was originally maintained by Google and can now be obtained from Github: > git clone https://github.com/sparsehash/sparsehash Follow the INSTALL notes for further details. Alternatively, sparsehash can be installed using apt-get: > apt-get install apt-get install libsparsehash-dev COMPILATION ----------- The src subdirecory contains the source files and two makefiles (Makefile and Makefile.csalign) that are needed to compile the cs-executables. To start the compilation, simply change into the src directory and execute any of the following commands: make csblast make csbuild make csclust make cssgd make cstrainset make cstranslate make -f Makefile.csalign csalign After the compilation has finished, the newly created executables can be found in the bin subdirectory. CONTEXT LIBRARIES ----------------- The data subdirectory contains the library of 4000 context profiles needed by CS-BLAST, as well as the CS62 column state alphabet for translating sequence profiles into CS62 sequences with cstranslate. - data/K4000.lib: context library of the generative model - data/K4000.crf: context library of the discriminative model REFERENCES ---------- Angermüller C., Biegert A., Söding J. (2012) Discriminative modelling of context-specific amino acid substitution probabilities.Bioinformatics 28(24): 3240-3247. PMID: 23080114 Biegert A., Söding J. (2009) Sequence context-specific profiles for homology search ing. Proceedings of the National Academy of Sciences 106(10): 3770-3775. PMCID: PMC2645910 CONTACT ------- Christof Angermueller, https://cangermueller.com, email@example.com soeding lab: http://www.mpibpc.mpg.de/soeding, firstname.lastname@example.org