Other servers

Server 2.1.0.A

Submit sequences

Comparison type: Scan Local Global
Enter two sequences in FASTA format
(Check data format and maximum sequence lengths here.)

or read both sequences from a FASTA file



General options
Maximum length difference (Delta) (max 25)
Gap opening cost (-50 recommended for global alignment)
Gap elongation cost (-25 recommended for global alignment)

Scanning options (Affect only scanning)
Maximum motif length (lambda) (max 200)
Maximum number of structures (max 10)

For publication of FOLDALIGN results, please cite

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix,
Havgaard JH, Torarinsson E, Gorodkin J. PLOS computational biology. 3:e193, 2007

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search,
J. H. Havgaard, R. B. Lyngsų, and J. Gorodkin. Nucleic Acids Research 33:W650-W653, 2005.

Comments, questions, etc., email webmaster@foldalign.kvl.dk.

Last updated September 27th, 2005 by Jakob Hull Havgaard