title: Visualization of near-optimal sequence alignments.
abstract: BACKGROUND
  Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.
  
  
  RESULTS
  We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.
authors.affiliation: Department of Systems and Information Engineering, University of Virginia, Charlottesville, VA 22908, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Smoot
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Guerlain
authors.forename: William R
authors.initials: WR
authors.lastname: Pearson
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D030562:Databases, Protein; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins