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ParasoR

Latest

2023.02.14 Update wiki to include the detail of Radiam (simulation of point mutation).

Features


ParasoR computes a variety of RNA secondary structure features for long RNA sequences even for human genome-level sequences by distributed computation using computer clusters.

Currently availabel features of ParasoR are

  • Base pairing probability (bpp)
  • Stem probability
  • Accessibility (loop probability)
  • Structure profiles (probability and motif sequence)
  • Single-core mode: Minimum free energy (MFE) structure γ-centroid structure
  • Multi-core mode: Maximum expected accuracy structure, which consists only the base pairs whose bpp is equal larger than 1/(1+γ))

  • γ-centroid structure with the color code of structure profiles.
  • Color: Exterior (light green), Stem (red), Bulge (orange), Multibranch (green), Hairpin (violet), Internal (blue).

Additionally, ParasoR simulates structure arrangements caused by a single point mutation.

Requirements

  • C++11

We already tested ParasoR running with Apple LLVM version 6.0 and GCC 4.8.1.

How to install

git clone https://github.com/carushi/ParasoR
cd ParasoR
./configure
make
make install

Another way without git is downloading the directory directly from "Download ZIP" button.

As a default, a 'double' option is valid for the precision of floating point. This setting can be changed by editting the line in the makefile as below.

make VAR=LONG
# use long double.
make VAR=SHORT
# use float.

If you have a trouble about automake setting, please try a handmade makefile as shown below.

cd src
make -f _Makefile

or

 autoreconf -ivf

Example

A shell script 'check.sh' can be used for a test run. This script is exected by typing the commands as follows.

cd script/
sh check.sh
cat ../doc/pre.txt
# stem probability based on previous algorithm (Rfold model)
cat ../doc/stem.txt
# stem probability based on ParasoR algorithm
python test.py
# Output numerical error between the result of ParasoR with single core and multiple core

To see more samples, please visit our wiki.

Reference

Citation

  • Kawaguchi R. et al. (2016) Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. BMC Bioinformatics, 17:203.

Algorithm

  • Kiryu H. et al. (2008) Rfold: an exact algorithm for computing local base pairing probabilities. Bioinformatics, 24 (3), 367–373.
  • Hamada M. et al. (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25 (4), 465-473.
  • Kiryu H. et al. (2011) A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. Bioinformatics, 27 (13), 1789-97.
  • Fukunaga T. et al. (2014) CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biol., 15 (1), R16.

Implementation

  • Hamada M. et al. (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25(4), 465–473.
  • Gruber AR. et al. (2008) The Vienna RNA websuite. Nucleic Acids Res., 36 (Web Server issue), W70–W74.

Energy model

  • Turner DH. et al. (2010) NNDB: the nearest neighbour parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res., 38(Database issue), D280–D282.
  • Andronescu M. et al. (2010) Computational approaches for RNA energy parameter estimation. RNA, 16(12), 2304–2318.

parasor's People

Contributors

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parasor's Issues

Autoconf didn't work

$ make install
...
WARNING: 'aclocal-1.15' is missing on your system.
...

This didn't help

$ make -f _Makefile

I used a workaround as follows

$ autoreconf -ivf

Why does ParasoR Read Parameter Files (e.g., one of Turner Model) at Repository?

Hi, the developer.

I'm using the software for getting base pairing probabilities of ncRNAs.
One installed at my own user directory (e.g., under the directory $HOME/prgrms) uses the above files on the downloaded repository (e.g., under the directory $HOME/dwnlds/parasor).
I think they should be installed into the same directory as the software. (For example, if I cleaned the repository, it wouldn't run properly saying there are missing files.)
Or there are configurable settings for achieving it although I read the output from the command $ ./configure --help under the repository?

And another question: the software could use multithreading? (For example, when using the parameter "--pre", it is computing in parallel?)
If not, since I think ParasoR is one of solutions of RNA secondary structure scalable to genome data, I'd like you to implement it.

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