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ProDA is a tool that constructs local multiple sequence alignments (MSAs) by first identifying repeated homologous regions in a collection of protein sequences.


Sequence analysis; Protein structure analysis; Protein folds and structural domains


  • Operation: Protein sequence analysis
  • Input: MFA
  • Output: ClustalW; FASTA
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1.0
  • Maturity: Stable
  • Credit: Fulbright fellowship, NDSEG fellowship, NSF CAREER Award.
  • Contact: phuongtm _at_ serafim _at_
  • Collection: -


Phuong TM, Do CB, Edgar RC, Batzoglou S "Multiple alignment of protein sequences with repeats and rearrangements." Nucleic Acids Res. 2006;34(20):5932-42.
PMID: 17068081
PMCID: PMC1635250

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