CopraRNA 2.1.3 – sRNA Target Prediction utilizing Homology

CopraRNA 2.1.3

:: DESCRIPTION

CopraRNA (Comparative Prediction Algorithm for sRNA Targets) is a tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

CopraRNA

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3487-96. doi: 10.1073/pnas.1303248110. Epub 2013 Aug 26.
Comparative genomics boosts target prediction for bacterial small RNAs.
Wright PR1, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J.

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

Linux / Windows / MacOsX
R package

:: 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.

homoTarget – Prediction of microRNA targets in Homo Sapiens

homoTarget

:: DESCRIPTION

HomoTarget is a new algorithm for prediction of microRNA targets in Homo sapiens.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

HomoTarget

:: MORE INFORMATION

Citation:

Genomics. 2012 Nov 19. pii: S0888-7543(12)00213-3. doi: 10.1016/j.ygeno.2012.11.005. [Epub ahead of print]
HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens.
Ahmadi H1, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, Masoudi-Nejad A

CapR 1.1.1 – Revealing Structural Specificities of RNA-binding protein Target Recognition

CapR 1.1.1

:: DESCRIPTION

CapR calculates probabilities that each RNA base position is located within each secondary structural context for long RNA sequences.

::DEVELOPER

Tsukasa Fukunaga

::REQUIREMENTS

Linux
Vienna RNA package

:: DOWNLOAD

CapR

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 21;15(1):R16. doi: 10.1186/gb-2014-15-1-r16.
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.
Fukunaga T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H.

TargetRank 1.0 – Rank Conserved and non-conserved microRNA Targets and siRNA off-targets

TargetRank 1.0

:: DESCRIPTION

TargetRank is a webtool for ranking conserved and non-conserved microRNA targets and siRNA off-targets.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. and Burge, C.G. (2007).
Determinants of targeting by endogeno us and exogenous microRNAs and siRNAs.
RNA 13, 1894-1910.

Targetfinder 1.7 – Predict Small RNA Targets in a Sequence Database

Targetfinder 1.7

:: DESCRIPTION

Targetfinder predicts small RNA targets in a sequence database using a plant-based scoring metric.

::DEVELOPER

the Carrington Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl

:: DOWNLOAD

Targetfinder

:: MORE INFORMATION

Citation:

Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. (2007)
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
PLoS ONE 2, e219.

GenemiR 1.0 – Unified Search of Mammalian microRNA Target Predictions

GenemiR 1.0

:: DESCRIPTION

The GenemiR software application is a tool aimed at biologists and bioinformaticians who wish to find prediction and expression patterns in sets of microRNAs and genes. The program works with mouse and human target prediction and expression data.

::DEVELOPER

Bertone Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

GenemiR

:: MORE INFORMATION

MDScan 2004 – Find Motif from ChIP-on-chip Targets

MDScan 2004

:: DESCRIPTION

MDScan (Motif Discovery scan) discovers conserved transcription factor binding sites among upstream sequences from chromatin immune precipitation experiments (CHIP) as well as from single microarray experiments. The algorithm is strictly deterministic, not discovering local minima and always giving the globally best conserved motif. It is faster than most other algorithms and nearly as sensitive as BioProspector.

MDScan Online Version

::DEVELOPER

Xiaole Shirley Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

windows with Cygwin / Linux / Mac OsX
C Complier

:: DOWNLOAD

MDScan

:: MORE INFORMATION

Citation:

Liu XS, Brutlag DL, Liu JS.
An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments.
Nat Biotechnol. 2002 20(8):835-9.

LabTargets – Keep Track & Report the Status of Targets & Complexes

LabTargets

:: DESCRIPTION

LabTargets, the tracker/browser/database for proteomics, is a small application for keeping track and report the status of targets and complexes in your laboratory.

::DEVELOPER

Jaime Prilusky at Weizmann Institute of Science

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Perl
Apache web server

:: DOWNLOAD

LabTargets

:: MORE INFORMATION

Help, FAQ, Support, Suggestions:
Send an email to jaime.prilusky@weizmann.ac.il