title: VISSA: a program to visualize structural features from structure sequence alignment.
abstract: BACKGROUND
  Multiple sequence alignment is an important tool to understand and analyze functions of homologous proteins. However, the logic of residue conservation/variation is usually apparent only in three-dimensional (3D) space, not on a primary sequence level. Thus, in a traditional multiple alignment it is often difficult to directly visualize and analyze key residues because they are masked by other residues along the alignment. Here we present an integrated multiple alignment and 3D structure visualization program that can (1) map and highlight residues from a 1D alignment onto a 3D structure and vice versa and (2) display only the alignment of preselected, key residues. This program, called Visualize Structure Sequence Alignment, also has many other built-in tools that can help analyze multiple sequence alignments.
  
  
  BACKGROUND
  http://bioinformatics.burnham.org/liwz/vissa
  
  
  BACKGROUND
  liwz@burnham.org.
authors.affiliation: Burnham Institute for Medical Research, La Jolla, CA 92037, USA. liwz@burnham.org
authors.forename: Weizhong
authors.initials: W
authors.lastname: Li
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
mesh_terms: D019295:Computational Biology; D003196:Computer Graphics; D017124:Conserved Sequence; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins