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Links tagged with 'arabidopsis'

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Found 28 links

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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
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tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

AGRISDatabase Content

http://arabidopsis.med.ohio-state.edu/

Model Organisms > Databases

The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.

NAR Database Issue 2011
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tagsarabidopsis gene regulatory networks genetic databases genetic promoter regions plant gene expression regulation transcription factors

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
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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
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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

euGenes: Genomic Information for Eukaryotic OrganismsDatabase Content

http://iubio.bio.indiana.edu:8089/

Model Organisms > General Resources

Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.

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tagsanimals arabidopsis caenorhabditis elegans chromosome mapping database management systems drosophila forecasting genetic databases genome humans mice saccharomyces sequence homology zebrafish

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
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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
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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

GeneSplicerTool Content

http://cbcb.umd.edu/software/GeneSplicer/

Expression > Splicing

A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice.

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tagsalgorithms alternative splicing arabidopsis computational biology dna factual databases genes human genome humans plant genome

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
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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

iCE - internet Contig ExplorerTool Content

http://www.bcgsc.ca/platform/bioinfo/software/ice

DNA > Mapping and Assembly
Model Organisms > General Resources

Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.

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tagsanimals arabidopsis caenorhabditis caenorhabditis elegans contig mapping dna fingerprinting helminth dna humans mice molecular cloning oryza sativa plant dna rats

iHOPTool Content

http://www.ihop-net.org/UniPub/iHOP/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.

NAR Web Server Issue 2007
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tagsanimals arabidopsis biology biomedical engineering caenorhabditis elegans computational biology database management systems drosophila melanogaster escherichia coli genes humans mice natural language processing periodicals as topic publications pubmed signal transduction software design zebrafish

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

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/

Expression > Splicing

The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

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tagsalgorithms arabidopsis artificial intelligence exons expert systems factual databases forecasting genetic models green fluorescent proteins introns luminescent proteins molecular sequence data neural networks (computer) plant dna plant rna reproducibility of results rna precursors rna splicing

OligoArrayTool Content

http://berry.engin.umich.edu/oligoarray2_1/

Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Model Organisms > General Resources

OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html

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tagsalgorithms arabidopsis gc rich sequence gene expression profiling genetic transcription nucleic acid conformation oligonucleotide array sequence analysis oligonucleotide probes plant genome thermodynamics

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