title: COBALT: constraint-based alignment tool for multiple protein sequences.
abstract: BACKGROUND
  A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools.
  
  
  RESULTS
  We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a collection of pairwise constraints derived from database searches, sequence similarity and user input, combines these pairwise constraints, and then incorporates them into a progressive multiple alignment. We show that using constraints derived from the conserved domain database (CDD) and PROSITE protein-motif database improves COBALT's alignment quality. We also show that COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems.
  
  
  BACKGROUND
  COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt
authors.affiliation: National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.
authors.forename: Jason S
authors.initials: JS
authors.lastname: Papadopoulos
authors.forename: Richa
authors.initials: R
authors.lastname: Agarwala
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins