JOY: protein sequence-structure representation and analysis

Bioinformatics. 1998;14(7):617-23. doi: 10.1093/bioinformatics/14.7.617.


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 ( ) and CAMPASS ( uk/campass). It has also been successfully used for identifying distant evolutionary relationships.

Availability: The program can be obtained via anonymous ftp from from the directory /pub/joy/. The address for the JOY server is


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Hydrogen Bonding
  • Molecular Sequence Data
  • Protein Conformation*
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Sequence Alignment
  • Software*


  • Proteins