BAliBASE

BAliBASE (Benchmark Alignment dataBASE) is a multiple sequence alignment (MSA) benchmarking reference set. It contains reference alignments based on three-dimensional structures and particular reference sets that contain various linear motifs. The AUthors also provide a program that can compare a test alignment with the BAliBASE reference alignment.

Topic

Phylogeny;Sequence analysis;Nucleic acid sites, features and motifs;Nucleic acid structure analysis;Sequence sites, features and motifs

Detail

  • Operation: Multiple sequence alignment

  • Software interface: Command-line user interface

  • Language: C

  • License: -

  • Cost: Free

  • Version name: 4 / 9

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Julie Thompson thompson@unistra.fr | Raymond Ripp raymond.ripp@unistra.fr

  • Collection: -

  • Maturity: -

Publications

  • BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.
  • Thompson JD, et al. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. 2005; 61:127-36. doi: 10.1002/prot.20527
  • https://doi.org/10.1002/prot.20527
  • PMID: 16044462
  • PMC: -
  • BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.
  • Bahr A, et al. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. 2001; 29:323-6. doi: 10.1093/nar/29.1.323
  • https://doi.org/10.1093/nar/29.1.323
  • PMID: 11125126
  • PMC: PMC29792

Download and documentation

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