Sequences

Fasta file (Max. size 150 Kbs)

Parameters

• Temperature: degrees Celcius (^oC)
• Sequence type: RNA DNA
• Sequence shape: Linear Circular
• d value: 0 1 2 3 4 5 6 7 8 9 10
• Minimun length: 1 2 3 4 5 6 7 8 9 10
• Sodium ion concentration: mol per liter
• Magnesium ion concentration: mol per liter
• Compute p_value? yes no
• Number of permutations for p_value computation: 10 100
• Threshold p_value: 0.1 0.05 0.01
• Permutation strategy: Mono-nucleotide shuffling Di-nucleotide shuffling
• Base-pairing threshold probability:

Please cite the following papers when using this website:

• 1. J. Y. Semegni; M. Wamalwa; R. Gaujoux; G. W. Harkins; A. Gray; D. P. Martin.
  NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments;
  Bioinformatics; Bioinformatics; 2011 27: 2443-244.
• Markham, N. R. & Zuker, M. (2008)
  UNAFold: software for nucleic acid folding and hybriziation.
  In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Function and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31.
  Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.