Source: conservation-code
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan@rostlab.org>,
           Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
               dh-python,
               python
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/conservation-code
Vcs-Git: https://salsa.debian.org/med-team/conservation-code.git
Homepage: http://compbio.cs.princeton.edu/conservation/

Package: conservation-code
Architecture: all
Depends: ${misc:Depends},
         ${python:Depends},
         python-numpy
Enhances: concavity
Description: protein sequence conservation scoring tool
 This package provides score_conservation(1), a tool to score protein sequence
 conservation.
 .
 The following conservation scoring methods are implemented:
  * sum of pairs
  * weighted sum of pairs
  * Shannon entropy
  * Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
    Valdar and Thornton 2001)
  * relative entropy with property groupings (Williamson 1995)
  * von Neumann entropy (Caffrey et al 2004)
  * relative entropy (Samudrala and Wang 2006)
  * Jensen-Shannon divergence (Capra and Singh 2007)
 .
 A window-based extension that incorporates the estimated conservation of
 sequentially adjacent residues into the score for each column is also given.
 This window approach can be applied to any of the conservation scoring
 methods.
 .
 The program accepts alignments in the CLUSTAL and FASTA formats.
 .
 The sequence-specific output can be used as the conservation input for
 concavity.
 .
 Conservation is highly predictive in identifying catalytic sites and
 residues near bound ligands.