The gsc-weighting package

[Tags:bsd3, library]

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.

Changes in version 0.2:

Changes in version 0.1.1.1:

Changes in version 0.1.1:

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 (==0.4.*) [details]
License BSD3
Author Felipe Almeida Lessa
Maintainer felipe.lessa@gmail.com
Stability Unknown
Category Clustering
Source repository head: darcs get http://patch-tag.com/r/felipe/gsc-weighting
Uploaded Sun Oct 30 18:46:13 UTC 2011 by FelipeLessa
Distributions NixOS:0.2.2
Downloads 1368 total (10 in the last 30 days)
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Status Docs uploaded by user
Build status unknown [no reports yet]

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