psRobot v1.2 – Plant Small RNA Analysis Toolbox

psRobot v1.2

:: DESCRIPTION

PsRobot is designed to analyze batch of plant small RNA data.

::DEVELOPER

Dr. Xiujie Wang’s “Omics” lab in the Institute for Genetics and Developmental Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • GCC

:: DOWNLOAD

  psRobot

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W22-8. doi: 10.1093/nar/gks554. Epub 2012 Jun 12.
PsRobot: a web-based plant small RNA meta-analysis toolbox.
Wu HJ, Ma YK, Chen T, Wang M, Wang XJ.

PEA-m5C 0.1.3 – An R package for Plant m5C analysis

PEA-m5C 0.1.3

:: DESCRIPTION

PEA-m5C is an accurate transcriptome-wide m5C modification predictor under machine learning framework

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

PEA-m5C

:: MORE INFORMATION

Citation

Song J, Zhai J, Bian E, Song Y, Yu J, Ma C.
Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning.
Front Plant Sci. 2018 Apr 18;9:519. doi: 10.3389/fpls.2018.00519. Erratum in: Front Plant Sci. 2018 Nov 30;9:1762. PMID: 29720995; PMCID: PMC5915569.

PEA v1.1 – Plant Epitranscriptome Analysis

PEA v1.1

:: DESCRIPTION

PEA is a docker-based integrated R toolkit that aims to facilitate the plant epitranscriptome analysis.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

PEA

:: MORE INFORMATION

Citation

Zhai J, Song J, Cheng Q, Tang Y, Ma C.
PEA: an integrated R toolkit for plant epitranscriptome analysis.
Bioinformatics. 2018 Nov 1;34(21):3747-3749. doi: 10.1093/bioinformatics/bty421. PMID: 29850798.

iwa-miRNA – Interactive Annotation of Plant MiRNAs

iwa-miRNA

:: DESCRIPTION

iwa-miRNA is a web-based platform for interactive annotation of plant miRNAs.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

iwa-miRNA 

:: MORE INFORMATION

Citation

Zhang T, Zhai J, Zhang X, Ling L, Li M, Xie S, Song M, Ma C.
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA.
Genomics Proteomics Bioinformatics. 2021 Jul 28:S1672-0229(21)00161-3. doi: 10.1016/j.gpb.2021.02.010. Epub ahead of print. PMID: 34332120.

comTAR – Conserved Plant miRNA Target Prediction Tool

comTAR

:: DESCRIPTION

comTAR is a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in different species.

::DEVELOPER

IBR (Instituto de Biología Molecular y Celular de Rosario)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 12. [Epub ahead of print]
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants.
Chorostecki U1, Palatnik JF.

PmiREN 2.0 – A comprehensive Encyclopedia of Plant miRNAs

PmiREN 2.0

:: DESCRIPTION

PmiREN (Plant miRNA ENcyclopedia) is a comprehensive functional plant miRNA database.

::DEVELOPER

Yang lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Guo Z, Kuang Z, Wang Y, Zhao Y, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T, Cao X, Wei J, Li L, Yang X.
PmiREN: a comprehensive encyclopedia of plant miRNAs.
Nucleic Acids Res. 2020 Jan 8;48(D1):D1114-D1121. doi: 10.1093/nar/gkz894. PMID: 31602478; PMCID: PMC6943064.

miRPlant v6 – An Integrated Tool for Identification of Plant MiRNA from RNA Sequencing Data

miRPlant v6

:: DESCRIPTION

miRPlant extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants.

::DEVELOPER

miRPlant team

:: SCREENSHOTS

miRPlant

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

 miRPlant

:: MORE INFORMATION

Citation

An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC:
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data.
BMC bioinformatics 2014, 15(1):275.

DARIO / plantDARIO – Web Server for the analysis of (Plant) Short RNAs

DARIO / plantDARIO

:: DESCRIPTION

DARIO is a free web server for the analysis of short RNAs from high throughput sequencing data.

plantDARIO is a free web server for the analysis of plant small non-coding RNAs from small RNA-Seq data.

::DEVELOPER

the Hoffmann Junior Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W112-7. doi: 10.1093/nar/gkr357. Epub 2011 May 27.
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.
Fasold M1, Langenberger D, Binder H, Stadler PF, Hoffmann S.

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.
Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF.
Front Plant Sci. 2014 Dec 23;5:708. doi: 10.3389/fpls.2014.00708. eCollection 2014.

TASSEL 5.0 / rTASSEL 0.9.23 – Association And Diversity Analyses In Plants And Animals

TASSEL 5.0 / rTASSEL 0.9.23

:: DESCRIPTION

TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information.

rTASSEL  construct an R-based front-end to connect to a variety of highly used TASSEL methods and analytical tools.

::DEVELOPER

The Buckler Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
  • / R

:: DOWNLOAD

 TASSEL / rTASSEL

:: MORE INFORMATION

Citation

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007)
TASSEL: Software for association mapping of complex traits in diverse samples.
Bioinformatics 23:2633-2635.

iTAK 1.7 – Plant Transcription Factor & Protein Kinase Identifier and Classifier

iTAK 1.7

:: DESCRIPTION

iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. Identification and classification of TFs and TRs are based on the rules (required and forbidden protein domains of each gene family) described in Perez-Rodriguez et al (2010).

::DEVELOPER

Fei Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl
  • Bioperl

:: DOWNLOAD

 iTAK

:: MORE INFORMATION

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