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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 15 links

ACTTool Content

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php [open in a new window]

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Expression > Transcript Expression Analysis
Model Organisms > Plants

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

links directory index: 96
TitlePublication YearGoogle Scholar Citation Count
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis200696
NAR Web Server Issue 2006
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tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

Adabidopsis eFP BrowserDatabase Content

http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi [open in a new window]

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Expression > Databases
Model Organisms > Plants

An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets (using example of Arabidopsis). Explores microarray and other data for hypothesis generation. eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets.

links directory index: 347
TitlePublication YearGoogle Scholar Citation Count
An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets2007347
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tagsanimals arabidopsis database management systems genetic databases humans mice microarray analysis visual perception
setsUniversity of Toronto

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/ [open in a new window]

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DNA > Annotations
Model Organisms > Plants
Sequence Comparison > Comparative Genomics

agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.

links directory index: 63
TitlePublication YearGoogle Scholar Citation Count
agriGO: a GO analysis toolkit for the agricultural community201063
NAR Web Server Issue 2010
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Arabidopsis EnsemblDatabase Content

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

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Model Organisms > Plants

Access to the Arabidopsis thaliana genome through the Ensembl user interface. There are two independent assemblies available, one from TIGR and one from MIPS. Includes the collection of NASC insertion mutants.

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AthaMapDatabase Content

http://www.athamap.de/ [open in a new window]

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Expression > Gene Regulation
Model Organisms > Plants

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

This content is being maintained by Reinhard Hehl.

links directory index: 116
TitlePublication YearGoogle Scholar Citation Count
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana20106
AthaMap, integrating transcriptional and post-transcriptional data200915
AthaMap web tools for the analysis and identification of co-regulated genes200725
AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana200524
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome200446
NAR Web Server Issue 2005
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AtSubPTool Content

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

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Model Organisms > Plants
Protein > Annotation and Function
Protein > Localization and Targeting

A highly accurate subcellular localization prediction tool for annotating the Arabidopsis thaliana proteome.

This content is being maintained by rkaundal.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis201013
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tagsamino acid sequence homology amino acids arabidopsis arabidopsis proteins artificial intelligence molecular sequence annotation Plant prediction protein databases protein sorting signals proteome roc curve species specificity subcellular fractions subcellular localization

Bio-Array Resource (BAR)Tool Content

http://bar.utoronto.ca/welcome.htm [open in a new window]

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DNA > DNA and Genomic Analysis
Model Organisms > Plants

The Bio-Array Resource for Plant Biology: user-friendly web-based tools for working with functional genomics and other data. Most are designed with the plant (mainly Arabidopsis) reseacher in mind, but a couple of them can be useful to the wider research community.

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setsUniversity of Toronto

Blast2GOTool Content

http://www.blast2go.org/ [open in a new window]

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DNA > Annotations
Model Organisms > Plants

The Blast2GO suite is a comprehensive bioinformatics tool for functional annotation of plant sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim.

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DATFDatabase Content

http://datf.cbi.pku.edu.cn [open in a new window]

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Expression > Gene Regulation
Model Organisms > Plants

The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
DATF: a database of Arabidopsis transcription factors2005164
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tagsamino acid sequence arabidopsis proteins database management systems molecular sequence data plant proteins protein databases transcription factors

DRTFDatabase Content

http://drtf.cbi.pku.edu.cn/ [open in a new window]

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Expression > Gene Regulation
Model Organisms > Plants

Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from <i>japonica</i> and <i>indica</i> rice genomes.

links directory index: 68
TitlePublication YearGoogle Scholar Citation Count
DRTF: a database of rice transcription factors200668
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tagsdatabase management systems oryza sativa protein databases transcription factors

ePlantDatabase Content

http://bar.utoronto.ca/eplant/ [open in a new window]

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Model Organisms > Other Organisms
Model Organisms > Plants

A suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. It can be applied to any model organism. Currently has 3 modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
ePlant and the 3D data display initiative: integrative systems biology on the world wide web20112
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tagsarabidopsis data display plants protein conformation single nucleotide polymorphism systems biology three-dimensional imaging
setsUniversity of Toronto

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences200337
NAR Web Server Issue 2003
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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

GABI-KatDatabase Content

http://www.gabi-kat.de/ [open in a new window]

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Model Organisms > Databases
Model Organisms > Plants

GABI-Kat: sequence-indexed collections of T-DNA insertion lines of Arabidopsis thaliana.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database20123
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GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main [open in a new window]

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DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses200619
NAR Web Server Issue 2006
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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

GeneCATTool Content

http://genecat.mpg.de [open in a new window]

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Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > Plants

The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants.

links directory index: 45
TitlePublication YearGoogle Scholar Citation Count
GeneCAT--novel webtools that combine BLAST and co-expression analyses200845
NAR Web Server Issue 2008
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tagsarabidopsis gene expression profiling gene regulatory networks glucosyltransferases hordeum lipids oligonucleotide array sequence analysis photosynthesis plant genes sequence alignment

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