RNA Sampler

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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:

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.


 

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).


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


Last updated May 20, 2004.        free web counter