Tag: Plant

PlantMAT v1.0 – Plant Metabolite Annotation Toolbox

PlantMAT v1.0

:: DESCRIPTION

PlantMAT is a computational tool combining library search and combinatorial enumeration to facilitate the structural identification of plant specialized metabolites, e.g., saponins and flavonoid glycosides.

::DEVELOPER

Sumner Research Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Excel

:: DOWNLOAD

PlantMAT

:: MORE INFORMATION

Citation

Qiu F, Fine DD, Wherritt DJ, Lei Z, Sumner LW.
PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications.
Anal Chem. 2016 Dec 6;88(23):11373-11383. doi: 10.1021/acs.analchem.6b00906. Epub 2016 Nov 23. PMID: 27934098.

psRNATarget – Plant small RNA Target Analysis Server

psRNATarget

:: DESCRIPTION

psRNATarget is a plant small RNA target analysis server, which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to “open” secondary structure around miRNA’s target site on mRNA.

::DEVELOPER

The Zhao Bioinformaitcs Lab at the Samuel Roberts Noble Foundation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W155-9. doi: 10.1093/nar/gkr319. Epub 2011 May 27.
psRNATarget: a plant small RNA target analysis server.
Dai X1, Zhao PX.

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.

pssRNAMiner – A Plant short small RNA Regulatory Cascade Analysis Server

pssRNAMiner

:: DESCRIPTION

pssRNAMiner is a novel web server  which is developed to identify both the clusters of phased small RNAs as well as the potential phase-initiator.

::DEVELOPER

The Zhao Bioinformaitcs Lab at the Samuel Roberts Noble Foundation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W114-8. doi: 10.1093/nar/gkn297. Epub 2008 May 12.
pssRNAMiner: a plant short small RNA regulatory cascade analysis server.
Dai X1, Zhao PX.

MirCompare 2.0 – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare 2.0

:: 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.

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.

PRGdb 2.0 – Plant Resistance Gene Analysis

PRGdb 2.0

:: DESCRIPTION

PRGdb is a web accessible open-source database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants.

::DEVELOPER

PRGdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • BioPerl
  • Berl
  • Apache web server
  • PHP

:: DOWNLOAD

 PRGdb

:: MORE INFORMATION

Citation

Walter Sanseverino, Antonio Hermoso, Raffaella D’Alessandro, Anna Vlasova, Giuseppe Andolfo, Luigi Frusciante, Ernesto Lowy, Guglielmo Roma, Maria Raffaella Ercolano
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants.
Nucleic Acids Res.: 2012;

Nucleic Acids Res. 2010 Jan;38(Database issue):D814-21. doi: 10.1093/nar/gkp978.
PRGdb: a bioinformatics platform for plant resistance gene analysis.
Sanseverino W, Roma G, De Simone M, Faino L, Melito S, Stupka E, Frusciante L, Ercolano MR.

AlphaPlantImpute – Phasing and Imputing Genotype data in Plant Breeding Populations

AlphaPlantImpute

:: DESCRIPTION

AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. Focal individuals can be descendants of a bi-parental cross at various levels of selfing or can be parents of one or more bi-parental populations. All information on the model of analysis, input files and their layout, is specified in a single parameter file.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

AlphaPlantImpute

:: MORE INFORMATION

Citation

Gonen S, Wimmer V, Gaynor RC, Byrne E, Gorjanc G, Hickey JM.
A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.
Theor Appl Genet. 2018 Nov;131(11):2345-2357. doi: 10.1007/s00122-018-3156-9. Epub 2018 Aug 4. PMID: 30078163; PMCID: PMC6208939.

PSI-predictor – Plant Subcellular Localization Prediction

PSI-predictor

:: DESCRIPTION

PSI-predictor (Plant Subcellular localization Integrative predictor) is currently the most comprehensive and integrative subcellular location predictor for plants. Based on the wisdom of group-voting and artificial neural network, PSI integrated prediction results from 11 individual predictors to give accurate results on cytosol (cytos), endoplasmic reticulum (ER), extracellular (extra), golgi apparatus (golgi), membrane (membr), mitochondria (mito), nuclear (nucl), peroxisome (pero), plastid (plast) and vacuole (vacu). The community outperformed each individual predictor both on every subcellular location (≥0.8) and overall, with an AUROC~0.932.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Lili Liu, Zijun Zhang, Qian Mei, Ming Chen (2013)
PSI: A comprehensive and integrative approach for accurate plant subcellular localization prediction,
PLoS One, DOI:10.1371/journal.pone.0075826

MTide – Identification of miRNA-target Interaction in Plants

MTide

:: DESCRIPTION

MTide is an integrated tool for the identification of miRNA-target interaction in plants. The core algorithm consists of a modified miRDeep2 and a modified CleaveLand4.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MTide

:: MORE INFORMATION

Citation

MTide: an integrated tool for the identification of miRNA-target interaction in plants.
Zhang Z, Jiang L, Wang J, Chen M.
Bioinformatics. 2014 Sep 24. pii: btu633.