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COBALT: constraint-based alignment tool for multiple protein sequences.

MOTIVATION: 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. AVAILABILITY: COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at:

Pubmed ID: 17332019


  • Papadopoulos JS
  • Agarwala R


Bioinformatics (Oxford, England)

Publication Data

May 1, 2007

Associated Grants

  • Agency: Intramural NIH HHS, Id:

Mesh Terms

  • Algorithms
  • Amino Acid Sequence
  • Molecular Sequence Data
  • Proteins
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Sequence Homology, Amino Acid
  • Software