Clustering

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

• a file containing the sequences to analyse in fasta format

The Chaotic Map Clustering algorithm performs a non-parametric hierarchical partition of data without prior assumptions about numbers of classes and geometric distribution of clusters; as a result, the hierarchical structure of data is obtained as a tree of clusters.

This service returns a GIF image representing a tree of clusters including their profiles. In addition, an URL to the image is returned in the output field 'legend'

$Rev: 20 $

Clustering service for gene expression patterns that runs the the following algorithms: SOTA, UPGMA, WPGMA, UPGMC, WPGMC, Single linkage, Complete linkage, SOM and K-means

$Rev: 20 $