COUSCOus: A Residue-Residue Contact Detecting Method

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Contact prediction using shrinked covariance (COUSCOus). COUSCOus is a residue-residue contact detecting method approaching the contact inference using the glassofast implementation of Matyas and Sustik (2012, The University of Texas at Austin UTCS Technical Report 2012:1-3. TR-12-29.) that solves the L_1 regularised Gaussian maximum likelihood estimation of the inverse of a covariance matrix. Prior to the inverse covariance matrix estimation we utilise a covariance matrix shrinkage approach, the empirical Bayes covariance estimator, which has been shown by Haff (1980) <DOI:10.1214/aos/1176345010> to be the best estimator in a Bayesian framework, especially dominating estimators of the form aS, such as the smoothed covariance estimator applied in a related contact inference technique PSICOV.

Author
Reda Rawi [aut,cre], Matyas A. Sustik [aut], Ben Calderhead [aut]
Date of publication
2016-02-28 16:26:52
Maintainer
Reda Rawi <rrawi@qf.org.qa>
License
GPL (>= 3)
Version
1.0.0

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Man pages

COUSCOus
Contact prediction using shrinked covariance.
COUSCOus-internal
Internal COUSCOus functions

Files in this package

COUSCOus
COUSCOus/inst
COUSCOus/inst/examples
COUSCOus/inst/examples/1oaiA0.fa
COUSCOus/src
COUSCOus/src/calculate_single_site_frequencies.c
COUSCOus/src/aa2num.c
COUSCOus/src/glassofast.f90
COUSCOus/src/form_covarience_matrix.c
COUSCOus/src/calculate_sequence_weights.c
COUSCOus/src/guess_rho_matrix.c
COUSCOus/src/calculate_pair_site_frequencies.c
COUSCOus/NAMESPACE
COUSCOus/R
COUSCOus/R/helper_preprocess.R
COUSCOus/R/helper_precision.R
COUSCOus/R/helper_shrinkage.R
COUSCOus/R/COUSCOus.R
COUSCOus/R/helper_prediction.R
COUSCOus/MD5
COUSCOus/DESCRIPTION
COUSCOus/man
COUSCOus/man/COUSCOus-internal.Rd
COUSCOus/man/COUSCOus.Rd