Software.ncrna.org: web servers for analyses of RNA sequences

We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif findings are available from the integrated web server and the individual stand-alone web servers. The servers are located at http://software.ncrna.org, along with the information for the evaluation and downloading. This website is freely available to all users and there is no login requirement.

[1]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[2]  Jan Gorodkin,et al.  Multiple structural alignment and clustering of RNA sequences , 2007, Bioinform..

[3]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[4]  Taishin Kin,et al.  miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. , 2007, RNA.

[5]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[6]  Yasuo Tabei,et al.  A fast structural multiple alignment method for long RNA sequences , 2008, BMC Bioinformatics.

[7]  Chuong B. Do,et al.  ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.

[8]  Kiyoshi Asai,et al.  Rfold: an exact algorithm for computing local base pairing probabilities , 2008, Bioinform..

[9]  Hiroshi Matsui,et al.  Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[10]  J. Ng,et al.  PseudoBase: a database with RNA pseudoknots , 2000, Nucleic Acids Res..

[11]  Gaurav Sharma,et al.  Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign , 2007, BMC Bioinformatics.

[12]  A. Wilm,et al.  A benchmark of multiple sequence alignment programs upon structural RNAs , 2005, Nucleic acids research.

[13]  Kiyoshi Asai,et al.  Stem Kernels for RNA Sequence Analyses , 2007, BIRD.

[14]  Kiyoshi Asai,et al.  Marginalized kernels for RNA sequence data analysis. , 2002, Genome informatics. International Conference on Genome Informatics.

[15]  Ian Holmes,et al.  Stem Stem Stem Stem Loop Loop Loop LoopLoop Loop Loop Loop Loop Loop Loop , 2005 .

[16]  Yasubumi Sakakibara,et al.  RNA secondary structural alignment with conditional random fields , 2005, ECCB/JBI.

[17]  Kiyoshi Asai,et al.  Robust prediction of consensus secondary structures using averaged base pairing probability matrices , 2007, Bioinform..

[18]  Yasuo Tabei,et al.  SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments , 2006, Bioinform..

[19]  Peter F. Stadler,et al.  Alignment of RNA base pairing probability matrices , 2004, Bioinform..

[20]  Aya Kojima,et al.  fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences , 2006, Nucleic Acids Res..

[21]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[22]  Yasuo Tabei,et al.  Murlet: a practical multiple alignment tool for structural RNA sequences , 2007, Bioinform..

[23]  Yasubumi Sakakibara,et al.  Pair hidden Markov models on tree structures , 2003, ISMB.

[24]  Taku Kudo,et al.  Mining frequent stem patterns from unaligned RNA sequences , 2006, Bioinform..