The gsc-weighting package
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.
Properties
| 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 | BSD3 |
| Author | Felipe Almeida Lessa |
| Maintainer | felipe.lessa@gmail.com |
| Category | Clustering |
| Uploaded | Tue Aug 3 03:11:42 UTC 2010 by FelipeLessa |
| Distributions | NixOS:0.2.2 |
| Downloads | 1531 total (16 in the last 30 days) |
| Votes | |
| 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 (included in the package)