RNA junctions are important structural elements of RNA molecules. They are formed by three or more helices coming together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we develop a web server, called CHSalign, for computing the secondary structure alignment of RNA molecules containing CHS motifs.
The web server has two versions: CHSalign_p and CHSalign_u.
CHSalign_p accepts as input two RNA secondary structures where the structures are not annotated with CHS motifs, and produces as output an optimal local alignment between the two RNA structures while taking into account their junctions and coaxial helical stacking in the junctions. This version is a pipeline, which invokes our previously developed Junction Explorer tool to automatically predict and identify the junctions and CHS motifs within the junctions in the input structures, and then aligns the input structures containing the CHS motifs. The output displays the predicted CHS motifs in the input structures in addition to aligned junctions and nucleotides. Click here to see a demo and to run the CHSalign_p program. Note: To predict and identify the junctions and CHS motifs within the junctions in a single structure R, please use two identical structures R and R as input of the CHSalign_p program, which will display the predicted CHS motifs in R.
CHSalign_u accepts as input two RNA secondary structures, both containing CHS motifs annotated manually by the user, and produces as output an optimal local alignment between the two annotated structures. Click here to see a demo and to run the CHSalign_u program.
The web server accepts input RNA data in three formats: Bpseq, CT and Vienna dot-bracket notation. Click here to see an introduction to the three data formats.
The web server does not handle pseudoknots. Pseudoknots in the example molecules on this website have been removed using the K2N tool.
Programs related to the web server can be downloaded here.
References:
Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason T. L. Wang and
Tamar Schlick.
CHSalign: a web server that builds upon Junction-Explorer and RNAJAG for
pairwise alignment of RNA secondary structures with coaxial helical
stacking.
PLoS One 2016;11(1):e0147097.
Christian Laing, Dongrong Wen, Jason T. L. Wang and Tamar Schlick.
Predicting coaxial helical stacking in RNA junctions.
Nucleic Acids Research 2012;40(2):487-498.