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.

TAPIR 1.2 – Prediction of Plant microRNA Targets

TAPIR 1.2

:: DESCRIPTION

TAPIR is a web server designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA – target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA – target duplex having a large loop, making them undetectable by traditional tools.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl
  • Bioperl
  • ViennaRNA library + perl modules

:: DOWNLOAD

 TAPIR

:: MORE INFORMATION

Citation

Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010)
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.
Bioinformatics 26, 1566-1568.

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.

LeafNet 0.0.1 – A CNN for Plant Identification

LeafNet 0.0.1

:: DESCRIPTION

LeafNet is a method based on a convolutional neural network (CNN) to identify plants from images of leaves.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

LeafNet

:: MORE INFORMATION

Citation

LeafNet: A computer vision system for automatic plant species identification
Author links open overlay panelPierreBarréaBen C.StöverbKai F.MüllerbVolkerSteinhagea
Ecological Informatics Volume 40, July 2017, Pages 50-56

SplamiR – Predicting miRNAs in Plants

SplamiR

:: DESCRIPTION

SplamiR is the first method for the prediction of spliced miRNAs in plants. It takes genomic sequence and the sequence of a potential target mRNA as input. In the first phase of SplamiR, a database of complementary sequence pairs is created for the given genomic sequence. These sequence pairs might encode for RNAs folding into stem-loop structures. In the second phase, this database is searched for sequences with complementarity to the given target mRNA. For the identified sequences, in silico splice variants are generated and these are classified as to whether they might represent pre-miRNAs.

::DEVELOPER

Theißen lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

  SplamiR

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 May 1;27(9):1215-23. doi: 10.1093/bioinformatics/btr132. Epub 2011 Mar 17.
SplamiR–prediction of spliced miRNAs in plants.
Thieme CJ, Gramzow L, Lobbes D, Theissen G.

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.

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