PcircRNA_finder – circRNA Prediction in Plants

PcircRNA_finder

:: DESCRIPTION

PcircRNA_finder is a software for circRNA prediction in plants.

::DEVELOPER

PcircRNA_finder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • Python

:: DOWNLOAD

 PcircRNA_finder

:: MORE INFORMATION

Citation:

PcircRNA_finder: a software for circRNA prediction in plants.
Chen L, Yu Y, Zhang X, Liu C, Ye C, Fan L.
Bioinformatics. 2016 Aug 4. pii: btw496.

MirCompare – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare

:: DESCRIPTION

MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs.

::DEVELOPER

MirCompare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction.
Pirrò S, Minutolo A, Galgani A, Potestà M, Colizzi V, Montesano C.
J Comput Biol. 2016 Jul 18.

ExactSearch – A Fast Plant Motif Search Tool

ExactSearch

:: DESCRIPTION

ExactSearch is a web tool which enables plant biologists to search for DNA motifs in the proximal promoters, and 3′ untranslated regions of all genes from 50 genome-sequenced plant species.

::DEVELOPER

ExactSearch team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ExactSearch: a web-based plant motif search tool.
Gunasekara C, Subramanian A, Avvari JV, Li B, Chen S, Wei H.
Plant Methods. 2016 Apr 28;12:26. doi: 10.1186/s13007-016-0126-6.

PlantMiRNAPred – Classification of Real and Pseudo Plant Pre-miRNAs

PlantMiRNAPred

:: DESCRIPTION

PlantMiRNAPred web server can be used to classify real plant pre-miRNAs and pseudo hairpins.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 15;27(10):1368-76. doi: 10.1093/bioinformatics/btr153. Epub 2011 Mar 26.
PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs.
Xuan P, Guo M, Liu X, Huang Y, Li W, Huang Y.

miRPlant v4 – An Integrated Tool for Identification of Plant MiRNA from RNA Sequencing Data

miRPlant v4

:: DESCRIPTION

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

::DEVELOPER

Systems Biology of Gene Regulatory Elements

:: 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.

PlantPhos – Plant Phosphorylation Prediction Tool

PlantPhos

:: DESCRIPTION

PlantPhos is a web tool for predicting potential phosphorylation sites in plant proteins.

::DEVELOPER

CSB Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity.
Lee TY, Bretaña NA, Lu CT.
BMC Bioinformatics. 2011 Jun 26;12:261. doi: 10.1186/1471-2105-12-261.

P-SAMS – the Plant Small RNA Maker Suite

P-SAMS

:: DESCRIPTION

P-SAMS is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants.

::DEVELOPER

the Carrington Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • C++ Compiler

:: DOWNLOAD

 P-SAMS

:: MORE INFORMATION

Citation:

P-SAMS: a web suite for plant artificial microRNA and synthetic trans-acting small interfering RNA design.
Fahlgren N, Hill ST, Carrington JC, Carbonell A.
Bioinformatics. 2015 Sep 17. pii: btv534

iTAK 1.5 – Plant Transcription Factor & Protein Kinase Identifier and Classifier

iTAK 1.5

:: 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

PlantTFcat – Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool

PlantTFcat

:: DESCRIPTION

PlantTFcat is a high-performance web-based plant transcription factor and transcriptional regulator categorization and analysis tool, designed to identify and categorize TFs and TRs in genome-scale protein or nucleic acid sequences.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 12;14:321. doi: 10.1186/1471-2105-14-321.
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool.
Dai X, Sinharoy S, Udvardi M, Zhao PX.

TASSEL 5.0 – Association And Diversity Analyses In Plants And Animals

TASSEL 5.0

:: 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.

::DEVELOPER

The Buckler Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 TASSEL

:: 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.