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.

CSTP 1.0 – Condition-specific Target Prediction from Motifs and Expression

CSTP 1.0

:: DESCRIPTION

CSTP is a computational tool to predict the TF-target regulation with expression data based on a philosophy of guilt by association. Different from other tools, CSTP does not insist on clear TF binding site in the promoters of target genes.The expression information of genes allows prediction of CSTP to be condition-specific or tissue-specific

::DEVELOPER

Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 27
Condition-specific target prediction from motifs and expression.
Meng G1, Vingron M.

PETModule – Motif Module based approach for Enhancer Target Prediction

 

PETModule

:: DESCRIPTION

PETModule is a software developed to find enhancer target gene (ETG) pairs through a motif module based approach. The output of the software is the enhancer target gene pairs with a probability score that measures how likely the predicted target gene is reliable. PETModule only needs enhancer locations to predict their target genes.

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Java

:: DOWNLOAD

PETModule

:: MORE INFORMATION

Citation:

Sci Rep. 2016 Jul 20;6:30043. doi: 10.1038/srep30043.
PETModule: a motif module based approach for enhancer target gene prediction.
Zhao C, Li X, Hu H.

HitPick – Hit Identification & Target Prediction of Chemical Screenings

HitPick

:: DESCRIPTION

HitPick is a web server that facilitates the analysis of chemical screenings by identifying hits and predicting their molecular targets.

::DEVELOPER

Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1910-2. doi: 10.1093/bioinformatics/btt303. Epub 2013 May 28.
HitPick: a web server for hit identification and target prediction of chemical screenings.
Liu X1, Vogt I, Haque T, Campillos M.

TargetThermo – microRNA Target Prediction under relaxed seed and no conservation requirements

TargetThermo

:: DESCRIPTION

The TargetThermo package uses an energy-based linear regression model to compute predicted expression fold change of a gene caused by a miRNA.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TargetThermo

:: MORE INFORMATION

RNAsnoop 0.2 – Target Prediction for H/ACA snoRNAs

RNAsnoop 0.2

:: DESCRIPTION

RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence. RNAsnoop implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant. Complemented by an support vector machine (SVM)-based machine learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information, it presents an efficient and reliable tool for the prediction of H/ACA snoRNA target sites. We apply RNAsnoop to identify the snoRNAs that are responsible for several of the remaining ‘orphan’ pseudouridine modifications in human rRNAs, and we assign a target to one of the five orphan H/ACA snoRNAs in Drosophila.

::DEVELOPER

Hakim Tafer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNAsnoop

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 1;26(5):610-6. Epub 2009 Dec 16.
RNAsnoop: efficient target prediction for H/ACA snoRNAs.
Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF.

MicroTar 0.9.6 – microRNA Target Prediction from RNA Duplexes

MicroTar 0.9.6

:: DESCRIPTION

MicroTar is a microRNA target prediction program based on mRNA sequence complementarity (3′-UTR seed matches) and RNA duplex energy prediction, assessing the impact of microRNA binding on complete mRNA molecules. It uses the RNAlib library from the Vienna RNA package.

::DEVELOPER

Tammi Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MicroTar Serial versionParallel (MPI) version

:: MORE INFORMATION

Citation:

Thadani R, Tammi MT (2006).
MicroTar: predicting microRNA targets from RNA duplexes
BMC Bioinformatics 7:S20.