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

 NO

:: 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.

MRPrimerW – Search valid Primers for multiple Targets of qPCR experiments without matching Off-targets

MRPrimerW

:: DESCRIPTION

The MRPrimerW server performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user.

::DEVELOPER

Infolab DGIST.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MRPrimerW

:: MORE INFORMATION

Citation

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.
Kim H, Kang N, An K, Koo J, Kim MS.
Nucleic Acids Res. 2016 May 6. pii: gkw380.

SI-FI 3.2 – RNAi (RNA interference) Off-target Prediction

SI-FI 3.2

:: DESCRIPTION

si-Fi (siRNA Finder) is a Software for RNAi (RNA interference) off-target prediction.The software is designed for checking long-double stranded RNAi constructs for target specificity and silencing efficiency. It can be used also to select sequence regions suitable for designing RNAi constructs. The program provides clear tabular and graphical outputs.

::DEVELOPER

Stefanie Lück

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SI-FI

:: MORE INFORMATION

Customized siDesigner – Design siRNA with Functional Off-target Filtering

Customized siDesigner

:: DESCRIPTION

Csidesigner (Customized siDesigner) is an siRNA selection tool with functional off-target filtering

::DEVELOPER

Jayprokas Chakrabarti lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Customized siDesigner

:: MORE INFORMATION

Citation:

Das S, Ghosal S, Kozak K, Chakrabarti J. (2012)
An siRNA designing tool with a unique functional off-target filtering approach.
J Biomol Struct Dyn. DOI: 10.1080/07391102.2012.736758

cnvOffSeq 0.1.2 – Detecting & Genotyping intergenic CNVs using off-target Exome data

cnvOffSeq 0.1.2

:: DESCRIPTION

cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.

::DEVELOPER

cnvOffSeq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux /Windows
  • Java

:: DOWNLOAD

 cnvOffSeq

:: MORE INFORMATION

Citation:

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.
Bellos E, Coin LJ.
Bioinformatics. 2014 Sep 1;30(17):i639-i645.

TALENoffer – Genome-wide TALEN Off-target Prediction

TALENoffer

:: DESCRIPTION

TALENoffer is a tool for genome-wide prediction of TAL effector nuclease (TALEN) off-target sites. TALENoffer is based on the same statistical model as TALgetter and features a substantially improved runtime, which allows for scanning complete genomes for TALEN off-target sites within a few minutes.

::DEVELOPER

Jstacs Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

  TALENoffer

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 15;29(22):2931-2. doi: 10.1093/bioinformatics/btt501. Epub 2013 Aug 30.
TALENoffer: genome-wide TALEN off-target prediction.
Grau J1, Boch J, Posch S.

CasOT 1.0 – CRISPR/Cas system (Cas9/gRNA) Off-Targeter

CasOT 1.0

:: DESCRIPTION

CasOT is a genome-wide potential Cas9/gRNA off-target searching tool.

::DEVELOPER

PKU Zebrafish Functional Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl
:: DOWNLOAD

 CasOT

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 21.
CasOT: a genome-wide Cas9/gRNA off-target searching tool.
Xiao A1, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, Zhang B.

Cas-OFFinder 1.1 – Off-target Searching tool

Cas-OFFinder 1.1

:: DESCRIPTION

Cas-OFFinder searches for potential off-target sites in a given genome or user-defined sequences.

::DEVELOPER

Genome Engineering Lab. Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 Cas-OFFinder 

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 15;30(10):1473-5. doi: 10.1093/bioinformatics/btu048. Epub 2014 Jan 24.
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases.
Bae S1, Park J, Kim JS.

OFF-TARGET PIPELINE 1.5.4.2 -Identify Off-targets of Pharmaceuticals

OFF-TARGET PIPELINE 1.5.4.2

:: DESCRIPTION

OFF-TARGET PIPELINE is a platform intended to carry out a recently introduced chemical systems biology approach for secondary target identification, but may also be useful to other applications in bioinformatics and drug discovery. Researchers can predict and compare protein functional sites, conduct structure-based docking, compute binding energy and compare electrostatic potential distribution within cavities. It also supports normalization of docking scores, information retrieval from PDB, and parsing of output files. All the afore-mentioned procedures are parallelized with significant speed gains and labor savings.

::DEVELOPER

Thomas Evangelidis (tevang3@gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 OFF-TARGET PIPELINE

:: MORE INFORMATION

References:

L. Xie, J. Wang and P.E. Bourne 2007
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators“.
PLoS Comp. Biol., 3(11):e217