CT-Finder 20160513 – A Web Service for CRISPR Optimal Target Prediction and Visualization

CT-Finder 20160513

:: DESCRIPTION

CT-Finder is a web service that allows a user to upload DNA sequences, set specifications according to experimental goals, and receive candidate guide RNA targets.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 CT-Finder

:: MORE INFORMATION

Citation

CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization.
Zhu H, Misel L, Graham M, Robinson ML, Liang C.
Sci Rep. 2016 May 23;6:25516. doi: 10.1038/srep25516.

RNA22 v2 – microRNA Target Detection

RNA22 v2

:: DESCRIPTION

RNA22 finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA.

::DEVELOPER

the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

RNA 22 full set of predictions  Batch submission tool

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Dec 15;28(24):3322-3. doi: 10.1093/bioinformatics/bts615. Epub 2012 Oct 16.
Interactive exploration of RNA22 microRNA target predictions.
Loher P1, Rigoutsos I.

pirnaPre 1.0.0 – piRNA Targets on mRNAs in Mouse

pirnaPre 1.0.0

:: DESCRIPTION

pirnaPre is a SVM classifier based on a combination of Miwi CLIP-Seq derived features and position derived features to predict potential targets of piRNAs on mRNAs.

::DEVELOPER

pirnaPre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pirnaPre

:: MORE INFORMATION

Citation

Computational identification of piRNA targets on mouse mRNAs.
Yuan J, Zhang P, Cui Y, Wang J, Skogerbø G, Huang DW, Chen R, He S.
Bioinformatics. 2015 Dec 16. pii: btv729.

TargetS – microRNA Target Prediction in Different Gene Regions

TargetS

:: DESCRIPTION

TargetS is a novel computational approach for predicting miRNA targets with the target sites located along entire gene sequences, which permits finding additional targets that are not located in the 3′ un-translated regions.

::DEVELOPER

Yin Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Python

:: DOWNLOAD

 TargetS

:: MORE INFORMATION

Citation

Identifying microRNA targets in different gene regions.
Xu W, San Lucas A, Wang Z, Liu Y.
BMC Bioinformatics. 2014;15 Suppl 7:S4. doi: 10.1186/1471-2105-15-S7-S4.

CapR 1.0.4 – Revealing Structural Specificities of RNA-binding protein Target Recognition

CapR 1.0.4

:: 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.

multiMiR 1.0.1 – Integration of microRNA-target Interactions along with their Disease and Drug Associations

multiMiR 1.0.1

:: DESCRIPTION

The R package multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs.

::DEVELOPER

Yuanbin Ru at Windber Research Institute & Katerina Kechris at the University of Colorado Denver.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 multiMiR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014;42(17):e133. doi: 10.1093/nar/gku631. Epub 2014 Jul 24.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.

sPARTA 1.12 – small RNA-PARE Target Analyzer

sPARTA 1.12

:: DESCRIPTION

sPARTA is a high performance software for the validation of plant miRNA or sRNA targets with PARE (Parallel Analysis of Read Ends) data.

miRferno is a target prediction module of sPARTA with standard and seed-free prediction modes.

::DEVELOPER

the Meyers lab at the University of Delaware.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 sPARTAmiRferno

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Oct;42(18):e139. doi: 10.1093/nar/gku693. Epub 2014 Aug 12.
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC

StarScan 1.2.0 – Scanning small RNA Targets from Degradome Sequencing data

StarScan 1.2.0

:: DESCRIPTION

StarScan (sRNA target Scan) is the first web server for discovering potential sRNA-mediated RNA cleavage events from degradome sequencing data in plants and animals. StarScan searches sRNA (miRNA, siRNA, piRNA, etc.) targets in annotated (lncRNAs, circRNAs, pseudogenes, 5′ UTR, CDS, 3′ UTR and introns) and unannotated genomic regions.

::DEVELOPER

miRlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

StarScan: a web server for scanning small RNA targets from degradome sequencing data.
Liu S, Li JH, Wu J, Zhou KR, Zhou H, Yang JH, Qu LH.
Nucleic Acids Res. 2015 May 18. pii: gkv524.

CopraRNA 2.0.3 – sRNA Target Prediction utilizing Homology

CopraRNA 2.0.3

:: 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.

TargetSpy 1.0 – microRNA Target Prediction

TargetSpy 1.0

:: DESCRIPTION

TargetSpy is a novel computational approach for predicting target sites regardless of the presence of a seed match.

::DEVELOPER

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 TargetSpy

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 28;11:292. doi: 10.1186/1471-2105-11-292.
TargetSpy: a supervised machine learning approach for microRNA target prediction.
Sturm M1, Hackenberg M, Langenberger D, Frishman D.