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

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld D, Havgaard JH, de Melo ACMA, Gorodkin J Bioinformatics 2015, 32(8):1238-1240
[ PubMed | Paper | Webserver | Software ]

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 ]