The Protomap program classifies proteins into clusters according to sequence similarity, using a combination of results from Smith-Waterman, FASTA and BLAST algorithms, and Blosum 50 and Blosum 62 similarity matrices. The clusters are taken at different levels of similarity and a hierarchy of clusters is built up. All proteins in SWISS-PROT have been classified in this manner. If not present in SWISS-PROT, any new protein of interest can be incorporated into the classification using the server. The different levels of clustering can be browsed through a tree-like structure.
Navigation is easy and the page design attractive. There is a guided tour and many help pages. When the search program runs, the different steps are clearly indicated on the screen. The results are easy to visualize and Java applets are provided to screen through the cluster tree organization or to see the alignment of two proteins.
The current version is Protomap 3.0, based on the latest release of SWISS-PROT (release 38).
Close and distant homologies can be investigated in an organized and intuitive manner. There are also links to structural and sequence motif databases.
Alignments can only be performed in a pairwise fashion and are shown in a schematic form that is difficult to understand.
Multiple alignments of the proteins in the different clusters would be welcome, at least for the ones that are highly related.