Foldalign: RNA Structure and Sequence Alignment

Server 2.5.1

Submit sequences

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

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 1000)
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 2007, 3(10):e193
[ PubMed | Paper | Software | Sup ]