SPARSE is a tool for the simultaneous alignment and folding of RNAs; similar to LocARNA, but with improved speed. Its asymptotic time complexity is equivalent to a sequence alignment algorithm (only quadratic time). Background on the novel SPARSE algorithm is given in our publication; complementary, we provide PDF slides (from the Benasque RNA meeting 2015.)
The software is freely available under GPL 3.0.
As a part of LocARNA package please follow the installation instructions of the LocARNA package.
The pairwise alignment tool sparse can be used to simultaneously align and fold two given sequences.
fileA.fa: > seqA ... [Your first RNA sequence] ... fileB.fa: > seqB ... [Your second RNA sequence] ...
Call sparse by:
sparse fileA.fa fileB.fa
For multiple alignment application, sparse inherits mlocarna progressive alignment approach, therefor one can do a multiple alignment with sparse by invoking mlocarna and mentioning sparse as the pairwise aligner tool.
file.fa: > seqA ... [Your first RNA sequence] ... > seqB ... [Your second RNA sequence] ...
Call sparse by passing the option --sparse to mlocarna:
mlocarna --sparse file.fa
Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, and Rolf
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 2015.
[pdf] [doi] [pubmed] [bib]