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README

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, cangermueller@ebi.ac.uk
soeding lab: http://www.mpibpc.mpg.de/soeding, soeding@mpibpc.mpg.de

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Context-specific mutation probabilities for protein sequencing searching.

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