Tag: RNAs

McGenus / TT2NE – Prediction of RNAs Secondary Structures with Pseudoknots

McGenus / TT2NE

:: DESCRIPTION

The McGenus and TT2NE algorithms output predictions of RNA secondary structures with pseudoknots, based on penalizing or restricting the topological genus of the pairing graphs. The topological genus is an indicator of the complexity of the topology of the pairing

::DEVELOPER

The Institut de Physique Théorique (IPhT)

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Feb 1;41(3):1895-900. doi: 10.1093/nar/gks1204. Epub 2012 Dec 16.
McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots.
Bon M1, Micheletti C, Orland H.

TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots.
Bon M, Orland H.
Nucleic Acids Res. 2011 Aug;39(14):e93. doi: 10.1093/nar/gkr240.

Off-Spotter 0.2.2 – very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

Off-Spotter 0.2.2

:: DESCRIPTION

Off-Spotteris a tool that when presented with a candidate gRNA and a PAM, quickly and exhaustively identifies all genomic sites that are identical or nearly-identical to the gRNA and also satisfy the PAM constraint.

::DEVELOPER

the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

Off-Spotter

:: MORE INFORMATION

Citation:

“Off-Spotter: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs“,
Venetia Pliatsika and Isidore Rigoutsos.
Biol. Direct. 2015;10 :4. doi: 10.1186/s13062-015-0035-z.

PCSHMM 1.1 – Structural Alignment of RNAs using Profile-csHMMs

PCSHMM 1.1

:: DESCRIPTION

PCSHMM (Profile-csHMM, Profile Context-Sensitive HMM) is a software for finding structural alignment of RNAs including pseudoknots based on profile-csHMMs

::DEVELOPER

Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 PCSHMM

:: MORE INFORMATION

Citation

Structural alignment of RNAs using profile-csHMMs and its application to RNA homology search: Overview and new results
Byung-Jun Yoon and P. P. Vaidyanathan,
IEEE Transactions on Circuits and Systems: Part-I, IEEE Transactions on Automatic Control (Joint Special Issue on Systems Biology), vol. 53, pp. 10-25, Jan. 2008.