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

Versions0.1, 0.1.0.1, 0.1.0.2, 0.1.1, 0.1.1.1, 0.2
Dependenciesbase (==4.*), hierarchical-clustering (==0.4.*)
LicenseBSD3
AuthorFelipe Almeida Lessa
Maintainerfelipe.lessa@gmail.com
CategoryClustering
Source repositoryhead: darcs get http://patch-tag.com/r/felipe/gsc-weighting
UploadedSun Oct 30 18:46:13 UTC 2011 by FelipeLessa
Downloads558 total (31 in last 30 days)
StatusDocs uploaded by user
Build status unknown [no reports yet]

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