LocARNA is a tool for multiple alignment of RNA molecules. LocARNA requires only RNA sequences as input and will simultaneously fold and align the input sequences. Specifications of additional constraints or fixed input structures are possible. LocARNA outputs a multiple alignment together with a consensus structure. For the folding it makes use of a very realistic energy model for RNAs as it is by RNAfold of the Vienna RNA package (or Zuker's mfold). For the alignment it features RIBOSUM-like similarity scoring and realistic gap cost. The LocARNA software is available for download as part of the LocARNA package (GPL 3).
LocARNA - Alignment & Folding
Try LocARNA with these examples:
When using LocARNA please cite :
- Sebastian Will, Tejal Joshi, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
RNA, 18 no. 5, pp. 900-14, 2012
- Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering
PLoS Computational Biology, 3 no. 4, pp. e65, 2007
- Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, and Rolf Backofen
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Nucleic Acids Research, 38, Suppl pp. W373-7, 2010
Results are computed with LocARNA version 1.8.5a linking Vienna RNA package 2.1.8