gsc-weighting: Generic implementation of Gerstein/Sonnhammer/Chothia weighting.
In their 1994 paper "Volume Changes in Protein Evolution", Gerstein, Sonnhammer and Chothia developed a weighting procedure for protein sequences to avoid over-represented sequences in the appendix "A Method to Weight Protein Sequences to Correct for Unequal Representation". Although their method was developed for protein sequences, it is readily extended to work on any measurable set.
This package calculates GSC weights for any reasonable
dendrogram. If you want to recreate their algorithm, then just
use UPGMA as linkage and residue identity as distance
function when creating the dendrogram.
| Versions | 0.1, 0.1.0.1, 0.1.0.2, 0.1.1, 0.1.1.1, 0.2, 0.2.1, 0.2.2 |
|---|---|
| Dependencies | base (==4.*), hierarchical-clustering (==0.*) [details] |
| License | BSD-3-Clause |
| Author | Felipe Almeida Lessa |
| Maintainer | felipe.lessa@gmail.com |
| Category | Clustering |
| Uploaded | by FelipeLessa at Tue Aug 3 03:11:42 UTC 2010 |
| Distributions | NixOS:0.2.2 |
| Downloads | 2643 total (13 in the last 30 days) |
| Rating | (no votes yet) [estimated by rule of succession] |
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| Status | Docs uploaded by user Build status unknown [no reports yet] Hackage Matrix CI |
Downloads
- gsc-weighting-0.1.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)