Cas-OFFinder 2.4.1 – Off-target Searching tool

Cas-OFFinder 2.4.1

:: 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.

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.

SI-FI 1.2.3 – RNAi (RNA interference) Off-target Prediction

SI-FI 1.2.3

:: 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

Citation

Lück S, Kreszies T, Strickert M, Schweizer P, Kuhlmann M, Douchkov D.
siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction.
Front Plant Sci. 2019 Aug 15;10:1023. doi: 10.3389/fpls.2019.01023. PMID: 31475020; PMCID: PMC6704232.

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.

GUIDEseq 1.20.0 – Identifying Off-targets with GUIDE-seq data

GUIDEseq 1.20.0

:: DESCRIPTION

GUIDEseq is a Bioconductor package for identifying off-targets with GUIDE-seq data. The package implements GUIDE-seq analysis workflow in a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

GUIDEseq

:: MORE INFORMATION

Citation:

Zhu LJ, Lawrence M, Gupta A, Pagès H, Kucukural A, Garber M, Wolfe SA.
GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.
BMC Genomics. 2017 May 15;18(1):379. doi: 10.1186/s12864-017-3746-y. PMID: 28506212; PMCID: PMC5433024.

MRPrimerW2 – Search valid Primers for multiple Targets of qPCR experiments without matching Off-targets

MRPrimerW2

:: 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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MRPrimerW

:: MORE INFORMATION

Citation

Jeon H, Bae J, Hwang SH, Whang KY, Lee HS, Kim H, Kim MS.
MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments.
Nucleic Acids Res. 2019 Jul 2;47(W1):W614-W622. doi: 10.1093/nar/gkz323. PMID: 31045205; PMCID: PMC6602510.

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.

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.

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