>
Tag
> Links tagged with 'plant genes'

Links tagged with 'plant genes'

RSS FeedCompact ViewList as XMLList as JSON

Found 21 links

Displaying 15 links

ACTTool Content

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php

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.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

agriGOTool Content

http://bioinfo.cau.edu.cn/agriGO/

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.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsagricultural crops plant genes

AHD2.0Database Content

http://ahd.cbi.pku.edu.cn/

Model Organisms > Databases

Arabidopsis Hormone Database (AHD) is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). AHD2.0 has new features: (i) updating our collection of AHRGs based on most recent publications as well as constructing elaborate schematic diagrams of each hormone biosynthesis and signaling pathways; (ii) adding orthologs of sequenced plants listed in OrthoMCL-DB to each AHRG in the updated database; (iii) providing predicted miRNA splicing site(s) for each AHRG; (iv) integrating genes that genetically interact with each AHRG according to literatures mining; (v) providing links to a powerful online analysis platform WebLab for the convenience of in-time bioinformatics analysis and (vi) providing links to widely used protein databases and integrating more expression profiling information that would facilitate users for a more systematic and integrative analysis related to phytohormone research.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis genetic databases micrornas plant genes plant growth regulators rna splicing

AthaMapDatabase Content

http://www.athamap.de/

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.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis arabidopsis proteins base sequence binding sites cold temperature computational biology conserved sequence dehydration genetic databases genetic transcription genomics molecular sequence data nucleic acid databases plant dna plant gene expression regulation plant genes plant genome protein binding response elements sequence alignment systems integration transcription factors transcriptional regulatory elements untranslated rna

GeneCATTool Content

http://genecat.mpg.de

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.

NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis gene expression profiling gene regulatory networks glucosyltransferases hordeum lipids oligonucleotide array sequence analysis photosynthesis plant genes sequence alignment

GeneSeqerTool Content

http://www.plantgdb.org/search/misc/PublicPlantSeq.php

DNA > Gene Prediction
Expression > Splicing
Model Organisms > Plants

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis complementary dna computational biology dna sequence analysis expressed sequence tags gene components genetic databases genetic transcription genomics nucleic acid repetitive sequences plant dna plant genes plant genome plant proteins plants protein sequence analysis sequence alignment

Gramene database in 2010Database Content

http://www.gramene.org

Model Organisms > Databases

The Gramene database has become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene has an Ensembl genome browser and host a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagschromosome mapping genetic databases genetic variation genomics metabolic networks and pathways plant genes plant genome plants quantitative trait loci synteny

GreenPhylDB v2.0Database Content

http://southgreen.cirad.fr/

DNA > Databases
Model Organisms > Databases

GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsgenetic databases genomics molecular sequence annotation phylogeny plant genes plant genome plant proteins plants

IccareTool Content

http://genopole.toulouse.inra.fr/bioinfo/Iccare/

Sequence Comparison > Other Alignment Tools

The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals arabidopsis chromosome mapping dna primers dna sequence analysis expressed sequence tags human genome humans messenger rna nucleic acid databases nucleic acid probes nucleic acid sequence homology plant genes rna sequence analysis rna splice sites systems integration

LSDDatabase Content

http://www.eplantsenescence.org/

Model Organisms > Databases

This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf senescence or morphological phenotypes. Users can browse or search the database to obtain information including literatures, mutants, phenotypes, expression profiles, miRNA interactions, orthologs in other plants and cross links to other databases.

This content is being maintained by luojc.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscell aging genetic databases molecular sequence annotation plant genes plant leaves sequence analysis

MIPSDatabase Content

http://mips.gsf.de/

Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans mice nucleic acid databases nucleic acid sequence homology oryza sativa plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology

miRUTool Content

http://bioinfo.noble.org/gateway/index.php?option=com_content&task=view&id=53&It...

Expression > Gene Regulation
RNA > Functional RNAs

miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms base pair mismatch messenger rna micrornas plant genes plant rna rna sequence analysis

PhosPhAtDatabase Content

http://phosphat.mpimp-golm.mpg.de/

Model Organisms > Databases

The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.

This content is being maintained by Waltraud Schulze.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis arabidopsis proteins binding sites computational biology genetic databases mass spectrometry phosphopeptides phosphoproteins phosphorylation phosphoserine plant genes plant genome protein databases protein sequence analysis

Plant Resistance Genes databaseDatabase Content

http://www.prgdb.org

Model Organisms > Databases

PRGdb is a database provides a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. Data can be examined using different query tools. A prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. The inferred cross-link between genomic and phenotypic information allows access to a large body of information.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscomputational biology gene expression profiling genetic databases nucleic acid databases oxidative stress plant diseases plant genes plant genome plants protein databases tertiary protein structure

PlnTFDBDatabase Content

http://plntfdb.bio.uni-potsdam.de/v3.0/

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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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