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SPARSE (Sparsified Prediction and Alignment of RNAs based on their structure Ensembles) is a tool to align RNA sequences based on structural properties of RNA ensembles. The SPARSE algorithm uses a Sankoff-style algorithm and runs in quadratic time without heuristics.


Nucleic acid structure analysis; Sequence analysis


  • Operation: Structure-based sequence alignment
  • Input: (RNA sequence): FASTA, FASTA-like txt
  • Output: (Alignment): PDF, FASTA, ClustalW, newick (tree), EPS (structure)
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 1.8.9
  • Maturity: Mature
  • Credit: The German Research Foundation. InKoMBio, German Federal Ministry of Education and Research
  • Contact: rna _at_ | will _at_ | rna _at_ | will _at_
  • Collection:


Will S, Otto C, Miladi M, Möhl M, Backofen R "SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics." Bioinformatics 2015; 31(15):2489-96
PMID: 25838465
PMCID: PMC4514930

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