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Plants

In this section are links specific to plant resources including those for Maize and Arabidopsis.

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Found 44 links

Displaying 14 links

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html [open in a new window]

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DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
PLecDom: a program for identification and analysis of plant lectin domains20096
NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

PLEXdbDatabase Content

http://www.plexdb.org/ [open in a new window]

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Expression > Databases
Model Organisms > Plants

Plant Expression Database is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
PLEXdb: gene expression resources for plants and plant pathogens20124
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PlnTFDBDatabase Content

http://plntfdb.bio.uni-potsdam.de/v3.0/ [open in a new window]

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Expression > Gene Regulation
Model Organisms > Plants

Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST.

links directory index: 171
TitlePublication YearGoogle Scholar Citation Count
PlnTFDB: updated content and new features of the plant transcription factor database201060
PlnTFDB: an integrative plant transcription factor database2007111
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tagscomputational biology gene regulatory networks genetic databases genetic promoter regions plant diseases plant gene expression regulation plant genes plant genome plant proteins plants protein databases sequence alignment tertiary protein structure transcription factors

PosMedTool Content

http://omicspace.riken.jp/PosMed/ [open in a new window]

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Human Genome > Health and Disease
Literature > Text Mining and Semantics
Model Organisms > Mouse and Rat
Model Organisms > Plants

To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based on direct and indirect inference of the hit documents. PosMed currently supports prioritization of positional cloning candidate genes in human, mouse, rat and Arabidopsis thaliana.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning200922
NAR Web Server Issue 2009
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PREP SuiteTool Content

http://prep.unl.edu/ [open in a new window]

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Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments200911
PREP-Mt: predictive RNA editor for plant mitochondrial genes200538
NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

PRI-CATTool Content

http://www.ab.wur.nl/pricat [open in a new window]

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Computer Related > Workflows
Expression > Gene Regulation
Model Organisms > Plants

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.

This content is being maintained by jose.muino@wur.nl.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments20115
NAR Web Server Issue 2011
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tagsarabidopsis binding sites ChIP-seq chromatin immunoprecipitation dna-binding proteins genetic promoter regions high-throughput nucleotide sequencing plant proteins plants transcription factors

psRNATargetTool Content

http://plantgrn.noble.org/psRNATarget/. [open in a new window]

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Model Organisms > Plants
RNA > Functional RNAs

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
psRNATarget: a plant small RNA target analysis server201127
NAR Web Server Issue 2011
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tagsmessenger rna micrornas plant gene expression regulation plant rna rna sequence analysis small interfering rna small untranslated rna

psRobotTool Content

http://omicslab.genetics.ac.cn/psRobot/ [open in a new window]

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Model Organisms > Plants
RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

psRobot is a web-based tool for plant small RNA meta-analysis. psRobot computes stem-loop small RNA prediction, which aligns user uploaded sequences to the selected genome, extracts their predicted precursors, and predicts whether the precursors can fold into stem-loop shaped secondary structure. psRobot also computes small RNA target prediction, which predict the possible targets of user provided small RNA sequences from the selected transcript library.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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pssRNAMinerTool Content

http://bioinfo3.noble.org/pssRNAMiner/ [open in a new window]

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Model Organisms > Plants
RNA > Functional RNAs

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
pssRNAMiner: a plant short small RNA regulatory cascade analysis server200812
NAR Web Server Issue 2008
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tagsgenomics micrornas plant gene expression regulation plant rna small interfering rna

RSLpredTool Content

http://www.imtech.res.in/raghava/rslpred/ [open in a new window]

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Model Organisms > Plants
Protein > Localization and Targeting

A subcellular localization prediction tool specifically developed for Rice (Oryza sativa) based on machine learning techniques.

This content is being maintained by rkaundal.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information200913
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tagsalgorithms amino acid sequence artificial intelligence computer simulation cytoplasm machine learning techniques molecular evolution organelles oryza sativa plant proteins plants protein databases protein sequence analysis Protein subcellular localization proteomics reproducibility of results Rice

TAIRDatabase Content

http://arabidopsis.org/ [open in a new window]

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Model Organisms > Databases
Model Organisms > Plants

The Arabidopsis Information Resource (TAIR): genome database for Arabidopsis thaliana. Central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools20127
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The Arabidopsis Information Resource (TAIR)Resource Content

http://www.arabidopsis.org/ [open in a new window]

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Model Organisms > Plants

Comprehensive resource for the scientific community working with Arabidopsis thaliana.

links directory index: 503
TitlePublication YearGoogle Scholar Citation Count
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community2003503
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external linksLink on Twitter
tagsarabidopsis arabidopsis proteins biological models genetic databases genetic polymorphism oligonucleotide array sequence analysis plant genome

WhETSTool Content

http://www.rothamsted.ac.uk/whets/ [open in a new window]

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DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching and Classification

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence200710
NAR Web Server Issue 2007
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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

YOGYTool Content

http://www.bahlerlab.info/YOGY/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

links directory index: 34
TitlePublication YearGoogle Scholar Citation Count
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms200634
NAR Web Server Issue 2006
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