conservation-code 20110309.0-1~ubuntu12.04.1 source package in Ubuntu


conservation-code (20110309.0-1~ubuntu12.04.1) precise-backports; urgency=low

  * No-change backport to precise (LP: #1168423)
 -- Felix Geyer <email address hidden>   Mon, 29 Apr 2013 18:27:03 +0200

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Uploaded by:
Felix Geyer on 2013-04-29
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Debian Med
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Precise backports on 2013-04-29 universe science


Precise: [FULLYBUILT] i386


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conservation-code_20110309.0.orig.tar.xz 19.1 KiB caef16e54abe983d591721aef34fa5f0fc051d1f2fce9ac5637a3681be37a993
conservation-code_20110309.0-1~ubuntu12.04.1.debian.tar.gz 6.6 KiB 49b1388b119a85a2ff4d3257d2512bedd574a1482a5ffb1eca21257d022f8434
conservation-code_20110309.0-1~ubuntu12.04.1.dsc 2.1 KiB ba19a7e4238fecbed04a685aa75e81723d612b927c12f6378b7613162de712c5

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Binary packages built by this source

conservation-code: protein sequence conservation scoring tool

 This package provides score_conservation(1), a tool to score protein sequence
 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
 The program accepts alignments in the CLUSTAL and FASTA formats.
 The sequence-specific output can be used as the conservation input for
 Conservation is highly predictive in identifying catalytic sites and
 residues near bound ligands.