Foldalign: RNA Structural Alignment
Download Foldalign 2.5 (current version)
- Foldalign version 2.5.3
Bug fixes affecting global alignments Download Change log - Foldalign version 2.5.2
Limits the default number of non-overlapping alignmnet regions for locateHits to 1.000, which makes locateHits significantly faster for long sequences. Based on long_sequences version of Foldalign. Download Change log - Foldalign version 2.5.1_long_sequences
A recompile of Foldalign 2.5.1 suiteable for long sequences. Can handle sequences longer than 30,000nt. Uses a constant factor more memory than the regular version 2.5.1. Download Change log - Foldalign version 2.5.1
A multithreaded version of Foldalign. Very minor update. This version will read files with lines ending with \r\n correctly. Download Change log - Foldalign version 2.5.0
This is the version used in Sundflet et al. paper A multithreaded version of Foldalign. Download Change log
Foldalign versions 2.0 and 2.1
- Foldalign version 2.1.1
Pairwise local or global alignment. This version uses the pruning heuristic and is therefore much faster and uses less memory than the previous version. Version 2.1.1 is a minor update to version 2.1.0. The difference is that 2.1.1 compiles with newer versions of gcc (g++). The alignments produced are the same as those produced by version 2.1.0.
Download - Foldalign version 2.1.0
Pairwise local or global alignment. This version uses the pruning heuristic and is therefore much faster and uses less memory than the previous version.
Download - Foldalign version 2.0.3
This version structurally align two sequences and can handle non-pseudoknotted structure using a light weight energy model in combination with RIBOSUM like score matrices.
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Download FoldalignM
- FoldalignM version 1.0.2
This version of FoldalignM uses version 2.1.5 of the Vienna RNA package. Note that this version can give slightly different results compared with earlier versions and the results of the Download Datasets - FoldalignM version 1.0.1
A multiple RNA structural RNA alignment method, to a large extend based on the PMcomp program.
Download Datasets
Citing
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J*
Bioinformatics. 2016 Apr 15;32(8):1238-40. Epub 2015 Dec 24
[ PubMed | Paper | Webserver | Software ]
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
Havgaard JH, Lyngso RB, Gorodkin J*
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3
[ PubMed | Paper | Webserver | Software | Sup ]
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