RNAMotif 3.1.1 – Find Structural Motifs in RNA

RNAMotif 3.1.1

:: DESCRIPTION

The rnamotif program searches a database for RNA sequences that match a “motif” describing secondary structure interactions. A match means that the given sequence is capable of adopting the given secondary structure, but is not intended to be predictive. Matches can be ranked by applying scoring rules that may provide finer distinctions than just matching to a profile.

::DEVELOPER

the Case group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window with Cygwin / Linux / Mac OsX
  • C-compiler

:: DOWNLOAD

RNAMotif

:: MORE INFORMATION

Citation

T. Macke, D. Ecker, R. Gutell, D. Gautheret, D.A. Case and R. Sampath.
RNAMotif — A new RNA secondary structure definition and discovery algorithm.
Nucl. Acids Res. 29, 4724-4735 (2001).

mCarts 1.2.0 – Hidden Markov model to predict Clustered RNA Motif sites

mCarts 1.2.0

:: DESCRIPTION

mCarts is a hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

::DEVELOPER

Zhang Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 mCarts

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.
Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
Zhang C1, Lee KY, Swanson MS, Darnell RB.

CompAnnotate 1.5 – Annotate base-pairing Interactions in RNA 3D Structures.

CompAnnotate 1.5

:: DESCRIPTION

CompAnnotate is a program for annotation of RNA using comparative method. A better annotation is generated for a low resolution ‘target PDB’ with the help of a high resolution ‘reference PDB’.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CompAnnotate

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2017 Aug 21;45(14):e136. doi: 10.1093/nar/gkx538.
CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.
Islam S, Ge P, Zhang S.

STAR3D 1.2 / WebSTAR3D / LocalSTAR3D v1 – Alignment of RNA 3D Structures

STAR3D 1.2 / WebSTAR3D / LocalSTAR3D v1

:: DESCRIPTION

STAR3D is a stack-based RNA 3D structural alignment tool.

WebSTAR3D is a web server for RNA 3D structure alignment

LocalSTAR3D is a program for the local alignment of RNA 3D structures.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

STAR3D / LocalSTAR3D

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Nov 16;43(20):e137. doi: 10.1093/nar/gkv697. Epub 2015 Jul 15.
STAR3D: a stack-based RNA 3D structural alignment tool.
Ge P, Zhang S.

Bioinformatics. 2016 Dec 1;32(23):3673-3675. Epub 2016 Aug 6.
WebSTAR3D: a web server for RNA 3D structural alignment.
Holzhauser E, Ge P, Zhang S

RNASLOpt – Predicting stable local optimal Structures for RNAs

RNASLOpt

:: DESCRIPTION

RNASLOpt is a program for predicting stable local optimal secondary structures (represented by stack configurations) for RNAs. RNASLOpt can be used to predict alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNASLOpt

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Nov 1;27(21):2994-3001. doi: 10.1093/bioinformatics/btr510. Epub 2011 Sep 8.
Finding stable local optimal RNA secondary structures.
Li Y, Zhang S.

RNAEAPath 1.0 – Predicting Folding Pathways between RNA Conformational Structures Guided by RNA Stacks

RNAEAPath 1.0

:: DESCRIPTION

RNAEAPath provides an alternate approach for predicting low-barrier folding pathways between RNA conformational secondary structures.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAEAPath

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S5. doi: 10.1186/1471-2105-13-S3-S5.
Predicting folding pathways between RNA conformational structures guided by RNA stacks.
Li Y, Zhang S.

RNAMotifScan 5.3 – Automatic Comparing and Searching for RNA Tertiary Motifs

RNAMotifScan 5.3

:: DESCRIPTION

RNAMotifScan is a tool for automatic comparing and searching for RNA tertiary motifs using secondary structural alignment.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • C Compiler

:: DOWNLOAD

 RNAMotifScan

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Oct;38(18):e176. doi: 10.1093/nar/gkq672. Epub 2010 Aug 8.
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.
Zhong C, Tang H, Zhang S.

ExonScan 1.0 – Simulating the RNA Splicing Pattern of a Primary Transcript Sequence

ExonScan 1.0

:: DESCRIPTION

ExonScan expects a primary transcript sequence, preferably excluding the first and last exon. It also currently needs at least about 20 bases upstream of the first exon it can locate, and at least about 60 bases downstream of the last. Numbers in the sequence are discarded, so you can cut and paste from, e.g., a GenBank file.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Cell. 2004 Dec 17;119(6):831-45.
Systematic identification and analysis of exonic splicing silencers.
Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB.

comRNA 1.80 – Common RNA Secondary Structure Predictor

comRNA 1.80

:: DESCRIPTION

comRNA is a new program that predicts common RNA secondary structure motifs in a group of related sequences.The algorithm applies graph-theoretical approaches to automatically detect common RNA secondary structure motifs in a group of functionally or evolutionarily related RNA sequences.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

comRNA

:: MORE INFORMATION

Citation:

Yongmei Ji, Xing Xu and Gary D. Stormo,
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
, Bioinformatics, 2004 Jul 10; 20(10):1591-1602.”

ILM 1.0 – Predict RNA Secondary Structures with Pseudoknots

ILM 1.0

:: DESCRIPTION

 ILM (Iterated Loop Matching) is a web server for predicting RNA secondary structures with pseudoknots.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C Compiler

:: DOWNLOAD

 ILM

:: MORE INFORMATION

Citation

Ruan J, Stormo GD and Zhang W.
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots“,
Bioinformatics. 2004 Jan 1;20(1):58-66.