JOY: protein sequence-structure representation and analysis

Motivation: JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments. Results: The JOY representation now constitutes an essential part of the two databases of protein structure alignments. HOMSTRAD (http://www-cryst.bioc.cam.ac.uk/similar to homstrad) and CAMPASS (http://www-cryst.bioc.cam.ac.uk/similar to campass). It has also been successfully used for identifying distant evolutionary relationships. Availability: The program can be obtained via anonymous ftp from torsa.bioc.cam.ac.uk fi om the directory /pub/joy/. The address for the JOY sewer is http://www-cryst. bioc.cam.ac.uk/cgi-bin/joy.cgi. Contact: kenji@cryst.bioc.cam.ac.uk.