conservation-code
protein sequence conservation scoring tool
Command lineScience
Not tested on a device yet. What that means
Commands in the package
score_conservation
About conservation-code
From Debian's package description
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.
From Debian's description of the conservation-code package, under that package's license.
Dependencies
Depends on
python3python3-numpy
Related apps
- hmmerprofile hidden Markov models for protein sequence analysisCommand line
- muscleMultiple alignment program of protein sequencesCommand line
- clustaloGeneral-purpose multiple sequence alignment program for proteinsCommand line
- wisecomparison of biopolymers, like DNA and protein sequencesCommand line
- prodamultiple alignment of protein sequencesCommand line
- hhsuitesensitive protein sequence searching based on HMM-HMM alignmentCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the conservation-code package, under that package's license.
- Description: Debian's description of the conservation-code package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.