sTarPicker – Global Target Prediction for Bacterial small non-coding RNAs

sTarPicker

:: DESCRIPTION

sTarPicker is a novel method for sRNA target prediction which was based on a two-step model for hybridization between an sRNA and an mRNA target.

::DEVELOPER

Prof. Wuju Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 sTarPicker

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(7):e22705. doi: 10.1371/journal.pone.0022705. Epub 2011 Jul 22.
sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.
Ying X1, Cao Y, Wu J, Liu Q, Cha L, Li W.

MIRPIPE 1.2.1 – miRNA detection and quantification pipeline

MIRPIPE 1.2.1

:: DESCRIPTION

MIRPIPE enables rapid and simple browser-based miRNA homology detection and quantification.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MIRPIPE

:: MORE INFORMATION

Citation:

MIRPIPE – quantification of microRNAs in niche model organisms.
Kuenne C, Preussner J, Herzog M, Braun T, Looso M.
Bioinformatics. 2014 Aug 26. pii: btu573.

PANGEA 1.0.2 – Pipeline Analysis for Next GEneration Amplicons

PANGEA 1.0.2

:: DESCRIPTION

PANGEA is a code useful for the analysis of 16S rRNA nucleotide sequences

::DEVELOPER

Austin Davis-Richardson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 PANGEA

:: MORE INFORMATION

Citation

ISME J. 2010 Jul;4(7):852-61. doi: 10.1038/ismej.2010.16. Epub 2010 Feb 25.
PANGEA: pipeline for analysis of next generation amplicons.
Giongo A1, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW.

ProbRNA 20131213 – Modeling RNA Structure Probing data

ProbRNA 20131213

:: DESCRIPTION

ProbRNA produces features found to be related to both the secondary and tertiary structures of the RNAs.

::DEVELOPER

Kevin Yuk-Lap Yip

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Perl
  • R Package

:: DOWNLOAD

 ProbRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 21.
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
Hu X1, Wong TK, Lu ZJ, Chan TF, Lau TC, Yiu SM, Yip KY.

miRComp – Composite MicroRNA Target Prediction

miRComp

:: DESCRIPTION

miRComp is a filtering step of putative microRNA targets through aggregating the predictions by several algorithms using two composite statistics – composite ranks and composite “p-values”

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRComp

:: MORE INFORMATION

Citation

Jin Zhou, Shili Lin, Vince Melfi, Joe Verducci (2006).
Composite MicroRNA Target Predictions and Comparisons of Several Prediction Algorithms.
MBI Technical Report No. 51.

MS2distance – Minimum Length MS2 Folding Trajectories

MS2distance

:: DESCRIPTION

MS2distance is an algorithms to compute the shortest MS2 folding trajectory between any two given RNA secondary structures.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Python

:: DOWNLOAD

MS2distance 

:: MORE INFORMATION

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.