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• What is RNA Sampler? 

   

  RNA Sampler is a sampling based program that predicts common RNA secondary structure motifs in a group of related sequences, developed by Xing Xu, Yongmei Ji, and Gary Stormo at Washington University in Saint Louis. 

   

  It is an implementation of the algorithms described in the paper "RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment" (Bioinformatics).  The program is written in C.

The algorithm applies a probabilistic sampling approach and combines intrasequence base pairing probabilities and intersequence base alignment probabilities to prediction consensus structure on two sequences.  It is extended by using a consistency-based method to incorporates pairwise structural information to predict the common structure conserved among multiple sequences. 

The advantages of this method are that it:

• does not require the presence of global sequence similarities (but can take advantage of it),

• does not require prior structural alignment,

• is able to detect pseudoknot structures.

PDF reprint of the paper:

Unofficial version: No typos (at least less typos) and color-white figure.

"RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment"

Official version: Bioinformatics with a few typos and black-white figures.

"RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment"

 and "Supplementary Material".

 

TEST DATA SETS:

1. Data sets of 10 Rfam families  and known structures (Cobalamin, gcvT, glmS, purine, RFN, sbox, THI, tRNA, U1, and yyob-ykoY), 100 randomly selected sets for each family.  (Used to generate Figure 4 in the paper.)

2. Data sets of 10 Rfam families with evenly distrubuted sequence identities  (Cobalamin, gcvT, glmS, purine, RFN, sbox, THI, tRNA, U1, and yyob-ykoY. Used to generate Figure 5 in the paper.)

3. CC, SPS, and SCI scores for (FoldalignM, RNAalifold, and RNASampler) and R scripts to generate Figure 5 in the paper.

• How does RNASampler work?

Xing Xu, Yongmei Ji, and Gary D. Stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Bioinformatics, August 2007; 23: 1883 - 1891.

If RNA Sampler is used in work that is published, please cite:
Xing Xu, Yongmei Ji, and Gary D. Stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Bioinformatics, August 2007; 23: 1883 - 1891.

Please send bug reports, requests, comments and suggestions to  Xing Xu (xingxu AT genetics.wustl.edu), Yongmei Ji (yji AT genetics.wustl.edu) and Gary Stormo (stormo AT genetics.wustl.edu).

• Download RNASampler

Unofficial version: No typos (at least less typos) and color-white figure.

"RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment"

Official version: Bioinformatics with a few typos and black-white figures.

"RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment"

and "Supplementary Material".

Source code for the latest version:    RNASampler v1.3

Instruction for installation and usage:    README.html

RNA Sampler development log:    updates

 

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Last updated May 20, 2004.