Just Another Classification of Proteins
JACOP is a robust clustering method for protein sequences which is designed to sidestep difficulties caused by the mechanisms by which protein sequences diverge, i.e. by simultaneous residue substitutions, insertions and/or deletions and whole domain reorganisations (duplications/swapping/fusion). It is based on random sampling of sub-sequences (probes) out of a set of input sequences. The probes are compared to the input sequences, after a normalisation step; the results are used to partition the input sequences into homogeneous groups of proteins.
For more information on JACOP, see Sperisen & Pagni (2005).
The JACOP web service uses the results of clustering the input proteins to predict which pairs are sufficiently closely related to share function.
