Software.ncrna.org

A portal site for web servers and software tools for sequence/structure analyses of non-conding RNAs

This portal site offers web servers and downloading of software tools of ncRNA.org for the analyses of RNA sequences and their structures. The secondary structures of the RNAs as well as their sequences are important for the comparison, clustering and the finding non-coding RNAs. The following software tools focus on the secondary structures for the analyses of RNAs.
We recommend the integrated web server, which also offers blat search of the input sequences on various genome sequences and mapping to UCSC GenomeBrowser for Functional RNA.
Brief explanations of the software tools are located below the following table. For more details and evaluations, click the corresponding links in the table.

Software	Function	Pseudo- knot	Download	Stand-alone Web Server	Integreated Web Server	Publication	Evaluation	Detail
SCARNA	Pairwise Structural Alignment	yes	N/A		SCARNA	Bioinformatics 2006 [1]	SCARNA	SCARNA
Murlet	Multiple Structural Alignment	no	C++ source code		Murlet	Bioinformatics 2007 [2]	Murlet	Murlet
MXSCARNA	Multiple Structural Alignment	no	C++ source code		MXSCARNA	BMC Bioinformatics 2008 [3]	MXSCARNA	MXSCARNA
RNAmine	Structural Motif Extraction	no	contact	N/A	RNAmine	Bioinformatics 2006 [4]	RNAmine	RNAmine
PHMMTS	Sequence-structure alignment	no	C++ source code		PHMMTS	Bioinformatics 2003 [5]	PHMMTS	PHMMTS
PSTAG	Sequence-structure alignment	yes	C++ source code		PSTAG	Bioinformatics 2005 [6]	PSTAG	PSTAG
SOKOS/CAN	Sequence Comparison (Kernel)	no	C source code	N/A	N/A	Genome Informatics 2002 [7]	See Publication	SOKOS/CAN
Stem Kernel	Sequence Comparison (Kernel)	no	C++ source code	N/A	N/A	Journal of Bioinformatics and Computational Biology 2007 [8]	See Publication	Stem Kernel
miRRim	miRNA prediction	no	source code	N/A	N/A	RNA 2007 [9]	miRRim	miRRim
McCaskill-MEA	Consensus Structure Prediction	no	C++ source code	N/A	N/A	Bioinformatics 2007 [10]	See Publication	N/A
Rfold	Local Base Pairing Probabilities	no	C++ source code	N/A	N/A	Bioinformatics 2007 [11]	Rfold	Rfold

SCARNA

SCARNA is a pairwise alignment tool that separately aligns 5' parts and 3' parts of the stem candidates with rough consideration of consistency. If you are not interested in pseudoknots, we recommend MXSCARNA.

Murlet and MXSCARNA

We have developed two software tools, Murlet and MXSCARNA, for structural multiple alignment of RNA sequences. Murlet is based on pair CFG (stochastic context-free grammar) with drastic reduction of computational costs. MXSCARNA is an extension of SCARNA to progressive alignment and applicable to RNA sequences longer than 5000 bases. (In the web server, length of sequences are restricted to 1000 bases. Please run MXSCARNA locally for longer sequences.)

RNAmine

RNAmine finds frequent stem patterns as the structural motifs of a set of RNA sequences using graph mining technique.

PHMMTS and PSTAG

PHMMTS and PSTAG are the tools for aligning RNA sequences of unknown secondary structures to RNA sequences with their known secondary structures. PHMMTS (pair hidden Markov models on tree structures) handles only pseudoknot-free structures and PSTAG (pair stochastic tree adjoining grammar) can accept pseudonotted structures.

SCARNA, Murlet, MXSCARNA, RNAmine, PHMMTS and PSTAG can be used in our integrated web server as well as their stand-alone web servers.

We offer source code distributions of following five more software tools.

SOCOS/CAN and Stem Kernel

Pairwise alignment is a standard method for comparing two biological sequences. We developed two tools for comparison of RNA sequences based on kernel methods, which are alternative approach for biological sequence comparison. SOCOS/CAN calculates marginalized kernel on SCFG (stochastic context free grammar) and Stem Kernel compares the sequences by the kernel based on all possible stem patterns.

miRRim

Predicting non-coding is a difficult task because general sequence patterns are not known. For specific families of non-coding RNAs, however, realistic predictions are possible. We developed miRRim, a tool finding conserved miRNAs.

McCaskill-MEA

McCaskill-MEA is a tool to predict the consensus secondary structures from given multiple alignments.

Rfold

Rfold calculates local base pairing probabilities. The algorithm uses no sliding-window and calculates "exact" base pairing probabilities for a limited distance of base pairs based on the full energy model of Vienna RNA package.

ncRNA.org