metaRNAmodules 1.0.2 – Automated RNA 3D Module Extraction and Modeling

metaRNAmodules 1.0.2

:: DESCRIPTION

metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  metaRNAmodules

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795.
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.

RNAmountAlign – RNA Sequence/Structure Alignment

RNAmountAlign

:: DESCRIPTION

RNAmountAlign is a novel algorithm for RNA sequence/structure pairwise alignment, that runs in O(n3) time and O(n2) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics as well as parameter fitting.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmountAlign

:: MORE INFORMATION

Citation:

PLoS One, 15 (1), e0227177 2020 Jan 24 eCollection 2020
RNAmountAlign: Efficient Software for Local, Global, Semiglobal Pairwise and Multiple RNA Sequence/Structure Alignment
Amir H Bayegan , Peter Clote

RNAsc – RNA Secondary Structure Prediction using SHAPE or inline-probing data

RNAsc

:: DESCRIPTION

RNAsc is a web server that computes RNA secondary structure with user-input chemical/enzymatic probing data, especially Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) or inline-probing data

::DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAsc

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(10):e45160. doi: 10.1371/journal.pone.0045160. Epub 2012 Oct 16.
Integrating chemical footprinting data into RNA secondary structure prediction.
Zarringhalam K1, Meyer MM, Dotu I, Chuang JH, Clote P.

RNAparametric – Computing the Probability of RNA Hairpin and Multiloop Formation

RNAparametric

:: DESCRIPTION

RNAparametric is the RNA parametric structure webserver.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • C Compiler

:: DOWNLOAD

 RNAparametric

:: MORE INFORMATION

Citation:

J Comput Biol. 2014 Mar;21(3):201-18. doi: 10.1089/cmb.2013.0148. Epub 2014 Feb 21.
Computing the probability of RNA hairpin and multiloop formation.
Ding Y1, Lorenz WA, Dotu I, Senter E, Clote P.

DIAL – 3-Dimensional RNA Structural Alignment and Motif Detection

DIAL

:: DESCRIPTION

DIAL is a web server for 3-dimensional RNA structural alignment (global and local) and for motif detection. DIAL (DIhedral ALignment) runs in time that is quadratic in input length by performing an alignment which accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity, (iii) nucleotide base-pairing similarity.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

DIAL

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

F. Ferre; Y. Ponty; W. A. Lorenz; Peter Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities ,
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W659-68. Epub 2007 Jun 13.

rnaifold 3.1 – RNA Inverse Folding and Molecular Design

rnaifold 3.1

:: DESCRIPTION

rnaifold is a web server that solves the RNA inverse folding problem, using constraint programming. Given a target RNA secondary structure, as well as optional nucleotide constraints, RNAiFold determines all (or a large number of) RNA sequences, whose minimum free energy structure is the target structure.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 rnaifold

:: MORE INFORMATION

Citation

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
Garcia-Martin JA, Dotu I, Clote P.
Nucleic Acids Res. 2015 May 27. pii: gkv460.

RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design
J.A. Garcia-Martin, P. Clote, I. Dotu,
Journal of Bioinformatics and Computational Biology ,DOI: 10.1142/S0219720013500017

RNAbor – Compute Structural Neighbors of an RNA Secondary Structure

RNAbor

:: DESCRIPTION

RNAbor is a web server to compute secondary structural neighbors of a given RNA structure.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E. Freyhult, V. Moulton, P. Clote.
RNAbor: A web server for RNA structural neighbors.
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W305-9. Epub 2007 May 25.

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.