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Links tagged with 'arabidopsis proteins'

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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
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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

AtPIDDatabase Content

http://www.megabionet.org/atpid/

Model Organisms > Databases
Protein > Databases

The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.

NAR Database Issue 2011
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tagsarabidopsis proteins molecular sequence annotation protein databases protein interaction mapping proteomics

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

LocDBDatabase Content

http://www.rostlab.org/services/locDB

Protein > Databases

LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Each database entry contains the experimentally derived localization in Gene Ontology (GO) terminology, the experimental annotation of localization, localization predictions by state-of-the-art methods and, where available, the type of experimental information. LocDB is searchable by keyword, protein name and subcellular compartment, as well as by identifiers from UniProt, Ensembl and TAIR resources.

NAR Database Issue 2011
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tagsarabidopsis proteins data mining humans intracellular space protein databases proteins

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.

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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

PAIRDatabase Content

http://www.cls.zju.edu.cn/pair/

Model Organisms > Databases

The predicted Arabidopsis interactome resource (PAIR) contains experimentally reported molecular interactions and predicted interactions in Arabidopsis thaliana. PAIR predicts interactions by a fine-tuned support vector machine model that integrates indirect evidences for interaction, such as gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms (interologs). PAIR features a user-friendly query interface, providing rich annotation on the relationships between two proteins. A graphical interaction network browser has also been integrated into the PAIR web interface to facilitate mining of specific pathways.

NAR Database Issue 2011
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tagsarabidopsis proteins protein databases protein interaction mapping

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

NAR Web Server Issue 2005
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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein 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
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tagsarabidopsis arabidopsis proteins binding sites computational biology genetic databases mass spectrometry phosphopeptides phosphoproteins phosphorylation phosphoserine plant genes plant genome protein databases protein sequence analysis

PLAN2LTool Content

http://zope.bioinfo.cnio.es/plan2l

Literature > Text Mining and Semantics
Model Organisms > Plants

A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.

NAR Web Server Issue 2009
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tagsarabidopsis arabidopsis agamous protein arabidopsis proteins systems integration transcription factors

The Arabidopsis Information Resource (TAIR)Resource Content

http://www.arabidopsis.org/

Model Organisms > Plants

Comprehensive resource for the scientific community working with Arabidopsis thaliana.

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tagsarabidopsis arabidopsis proteins biological models genetic databases genetic polymorphism oligonucleotide array sequence analysis plant genome

TRANSFACDatabase Content

http://www.gene-regulation.com/pub/databases.html#transfac

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

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tagsanimals arabidopsis arabidopsis proteins binding sites database management systems developmental gene expression regulation dna dna-binding proteins drosophila melanogaster drosophila proteins eukaryotic cells factual databases gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans mice nucleic acid regulatory sequences rats saccharomyces systems integration tertiary protein structure tissue distribution transcription factors