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Links tagged with 'plant proteins'

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DATFDatabase Content

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

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.

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tagsamino acid sequence arabidopsis proteins database management systems molecular sequence data plant proteins protein databases transcription factors

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

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

Loc3DDatabase Content

http://cubic.bioc.columbia.edu/db/LOC3d/

Protein > Localization and Targeting

LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology amino acids animals chloroplasts computational biology computer simulation eukaryotic cells humans neural networks (computer) nuclear localization signals plant proteins protein conformation protein databases protein sequence analysis protein transport proteins proteome reproducibility of results secondary protein structure sequence alignment subcellular fractions

PFPTool Content

http://pfp.technion.ac.il/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PICTool Content

http://crick.mbu.iisc.ernet.in/~PIC/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.

NAR Web Server Issue 2007
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tagsamino acids animals computational biology humans hydrogen bonding molecular conformation molecular models molecular structure plant proteins protein databases proteins

PlantTFDB 2.0Database Content

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

Model Organisms > Databases

The PlantTFDB 2.0 plant transcription factor (TF) database contains detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well as cross references to various databases and literature citations for these TFs. Multiple sequence alignments and phylogenetic trees for each family can be shown as Weblogo pictures or downloaded as text files.

This content is being maintained by luojc.

NAR Database Issue 2011
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tagsmolecular sequence annotation phylogeny plant proteins protein databases transcription factors

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

PREP SuiteTool Content

http://prep.unl.edu/

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.

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

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

Sol Genomics NetworkDatabase Content

http://solgenomics.net/

Model Organisms > Databases

The Sol Genomics Network (SGN) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools.

NAR Database Issue 2011
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tagsgene expression profiling genetic databases genomics lycopersicon esculentum plant genome plant proteins

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

Swiss-Prot and TrEMBLDatabase Content

http://us.expasy.org/sprot/

Protein > Sequence Data

Swiss-Prot is a curated database of protein sequences that are highly annotated and have a minimal level of redundancy. TrEMBL is a supplement to Swiss-Prot, containing computer-annotated translations of EMBL sequences.

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tagsanimal models animals archaeal proteins bacterial proteins humans plant proteins protein databases proteins proteome proteomics systems integration terminology as topic

The Mendel SiteTool Content

http://mendel.imp.ac.at/

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

NAR Web Server Issue 2003
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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins