Regular language based constrained sequence alignment

Protein PAM250
Protein Blosum62
Alphanumeric LCS
Alphanumeric edit-distance

Algorithm of Arslan (2007)
Algorithm of Chung, Lu and Tang (2007)
Our algorithm based on Steiner trees
Our algorithm based on SLPs (4-Russians)

  • This application was developed for the paper: "G. Kucherov, T. Pinhas, and M. Ziv-Ukelson.: Regular language constrained sequence alignment revisited. Journal of Computational Biology, 18(5):771-781, 2011."
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RNA Structure Prediction
RNA Structural Alignment
Constrained Sequence Alignment
RNA Structural Search