title: JAE: Jemboss Alignment Editor.
abstract: One of the most basic methods of understanding the biological significance of a sequence is to produce an alignment with related sequences. A vital aspect of correctly aligning sequences is to apply biological intuition through manual editing of an alignment produced by multiple-sequence alignment software. As part of the European Molecular Biology Open Source Software Suite (EMBOSS), a new alignment editor in the Jemboss package is freely available for download. The Jemboss Alignment Editor (JAE) incorporates standard methods of editing, and colouring residues and nucleotides to highlight important regions of interest. JAE also makes use of scoring matrices (PAM and BLOSUM), selected by the user, to display regions of high degrees of similarity and identity. Other tools include the ability to calculate a consensus, a consensus plot (using a selected scoring matrix) and pairwise identities.
  
  
  BACKGROUND
  The JAE can be launched from the webpage (http://emboss.sourceforge.net/Jemboss/).
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. tjc@sanger.ac.uk
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Carver
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Mullan
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D004282:Documentation / Q000379:methods; D008969:Molecular Sequence Data; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins