Structure alignment software tools | RNA data analysis
The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures.
Allows multiple alignment of RNA molecules. CARNA does not pick the most likely consensus structure, but computes the alignment that fits best to all likely structures simultaneously. Hence, CARNA is particularly useful when aligning RNAs like riboswitches, which have more than one stable structure. Also, CARNA is not limited to nested structures, but is able to align arbitrary pseudoknots. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures. Alternatively, users can also provide base pair probability matrices (dot plots in .ps format) or fixed structures (as annotation in the FASTA alignment) for the input sequences.
A web tool that can be used to align two or more RNA tertiary structures. In SARSA, two RNA structural alignment tools are provided: 1) PARTS for pairwise alignment of RNA tertiary structures and 2) MARTS for multiple alignment of RNA tertiary structures. Both tools in SARSA take as input RNA 3D structures in the PDB format and in their outputs provide graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA molecules.
Formulates non-coding RNA (ncRNA) structural alignment problem as an extended chain problem. Chain-RNA is a program that is able to find local structural alignments between long genomic sequences. The main goal of ncRNA search is to locate the positions of ncRNA genes hidden in long genomic sequences. This tool can be used to search annotated homologous ncRNAs in genomic sequences and evaluated its sensitivity and false positive rate.
Supplies an ecosystem for RNA multiple sequence alignment editing. RALEE can mark-up the alignment based on the prediction of its consensus secondary structure. It provides such a colouring scheme allowing the user to colour the alignment more conventionally by conservation or residue identity. Other features permit users to integrate secondary structure predictions of arbitrary sequences in the alignment and to test how the alignment matches the new structure prediction.
Allows alignment of RNA sequences with conserved secondary structures. R-Coffee which is a part of the T-Coffee web server, allows creation of multiple RNA alignments that automatically take predicted secondary structure into account. The software uses as templates RNA secondary structure predictions obtained by applying the RNAplfold prediction algorithm on the sequences of interest. Users can choose between the slow and accurate mode.
An implementation of a pairwise stochastic context-free grammar for RNA structural alignment. We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. The proposed grammar is both structurally unambiguous and alignment unambiguous.
Simulates multiple alignments of a given average dinucleotide content. SISSIz implements an efficient algorithm to randomize multiple alignments preserving dinucleotide content. It can be used to get more accurate estimates of false positive rates of existing programs, to produce negative controls for the training of machine learning based programs, or as standalone RNA gene finding program. Currently this software implements a mono and dinucleotide model which should be sufficient for many applications.