title: INTERALIGN: interactive alignment editor for distantly related protein sequences.
abstract: Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the 'twilight zone', i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon alpha traces of corresponding protein structures. Profile alignment, using CLUSTALW, is implemented to improve the alignment of a sequence of unknown structure with the visually optimized structural alignment as compared with a standard multiple sequence alignment. Tree-based ordering further helps in identifying the structure closest to a given sequence.
authors.affiliation: Commissariat à I'Energie Atomique, CEA VALRTTO, DSV-DIEP-SBTN, Service de Biochimie post-génomique & Toxicologie Nucliaire Bagnols-sur-Cèze, France. olivier.pible@cea.fr
authors.forename: Olivier
authors.initials: O
authors.lastname: Pible
authors.forename: Gilles
authors.initials: G
authors.lastname: Imbert
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Pellequer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins