TREMOLO-HCA (Traveling into REmote hoMOLOgy with HCA) is a tool for the analysis of distant relationships between protein sequences. It allows an easier interpretation of the PSI-BLAST results by adding information on the domain architecture (deduced from the CDD database) of proteins with which the query sequence is aligned, as well on the conservation of hydrophobic amino acids that may be critical for the fold. HCA plots of the aligned sequences can also be displayed, allowing their comparison at the 2D level.
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Bioinformatics. 2013 Jul 15;29(14):1726-33. doi: 10.1093/bioinformatics/btt271. Epub 2013 May 14.
Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.
Faure G1, Callebaut I.