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Links tagged with 'plants'

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FMMTool Content

http://FMM.mbc.nctu.edu.tw/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.

NAR Web Server Issue 2009
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tagsbacteria factual databases metabolic networks and pathways pharmaceutical preparations plants

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
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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

GObletTool Content

http://goblet.molgen.mpg.de/

Protein > Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences

GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.

NAR Web Server Issue 2004NAR Web Server Issue 2003
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tagsanimals complementary dna dna sequence analysis genes humans invertebrates mice plants protein databases protein sequence analysis proteins reproducibility of results sequence homology terminology as topic

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
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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
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tagsgenetic databases genomics molecular sequence annotation phylogeny plant genes plant genome plant proteins plants

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

ITS2Database Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?search

DNA > Databases

The ITS2 Database holds information about sequence, structure and taxonomic classification of all internal transcribed spacer 2 (ITS2) in GenBank. ITS2 can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs.

NAR Database Issue 2010
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tagsbase sequence computational biology fungal genome fungi genetic databases molecular sequence data nucleic acid databases nucleic acid sequence homology plant genome plants ribosomal spacer dna tertiary protein structure

Plant MicroRNA DatabaseDatabase Content

http://bioinformatics.cau.edu.cn/PMRD

Model Organisms > Databases

The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, the possible target genes for each miRNA with a predicted interaction site are included in the database. In some instances, miRNA expression profiles are included in the PMRD.

NAR Database Issue 2010
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tagscomputational biology gene expression profiling genetic databases micrornas nucleic acid databases plant gene expression regulation plant genome plants protein databases species specificity tertiary protein structure

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
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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.

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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

PlnTFDBDatabase Content

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

Model Organisms > Databases

The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

NAR Database Issue 2010
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tagscomputational biology gene regulatory networks genetic databases plant diseases plant gene expression regulation plant genes plant genome plant proteins plants protein databases tertiary protein structure transcription factors

PRI-CATTool Content

http://www.ab.wur.nl/pricat

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.

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

SALADDatabase Content

http://salad.dna.affrc.go.jp/salad/en/

Model Organisms > Databases
Protein > Databases

SALAD is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available.

NAR Database Issue 2010
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tagsamino acid motifs computational biology genetic databases genetic markers genomics nucleic acid databases phylogeny plant genes plant genome plants protein databases species specificity