Institute of Computer Science
University Freiburg

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs


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.)


SPARSE is distributed as part of the LocARNA package. Please download from the package web page.


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.

> seqA 
... [Your first RNA sequence] ... 

> 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.

> 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 Backofen.
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 2015.
[pdf] [doi] [pubmed] [bib]