gsc-weighting: Generic implementation of Gerstein/Sonnhammer/Chothia weighting.

[ bsd3, clustering, library ] [ Propose Tags ]
Versions 0.1,,, 0.1.1,, 0.2, 0.2.1, 0.2.2
Dependencies base (==4.*), hierarchical‑clustering (==0.*) [details]
License BSD-3-Clause
Author Felipe Almeida Lessa
Category Clustering
Uploaded by FelipeLessa at Tue Aug 3 12:12:37 UTC 2010
Distributions NixOS:0.2.2
Downloads 2622 total (25 in the last 30 days)
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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.




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