Foldalign: RNA Structure and Sequence Alignment

Server 2.5.0

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

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J Bioinformatics. 32:1238-40, 2016
[ PubMed | Paper | Webserver | Software ]

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
Havgaard JH, Torarinsson E, Gorodkin J PLoS Comput Biol. 3:1896-908, 2007
[ PubMed | Paper | Software | Sup ]