Plants

In this section are links specific to plant resources including those for Maize and Arabidopsis.

Found 29 links

Displaying 15 links

ACTTool Content

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

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.

agriGOTool Content

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

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.

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Arabidopsis EnsemblDatabase Content

http://atensembl.arabidopsis.info/

Access to the Arabidopsis thaliana genome through the Ensembl user interface. There are two independent assemblies available, one from TIGR and one from MIPS. Includes the collection of NASC insertion mutants.

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Blast2GOTool Content

http://www.blast2go.org/

The Blast2GO suite is a comprehensive bioinformatics tool for functional annotation of plant sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim.

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DATFDatabase Content

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

The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.

DOE Joint Genome Institute Genome PortalDatabase Content

http://genome.jgi-psf.org/

The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.

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DRTFDatabase Content

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

Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from <i>japonica</i> and <i>indica</i> rice genomes.

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

GeneCATTool Content

http://genecat.mpg.de

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.

GeneMANIATool Content

http://www.genemania.org

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

Genome Database for RosaceaeDatabase Content

http://www.rosaceae.org/

Genome Database for Rosaceae (GDR) contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map.

Tags associated with subcategory 'Model Organisms/Plants'

sequence alignment computational biology arabidopsis plant genes genetic databases plant genome transcription factors genomics protein databases arabidopsis proteins animals expressed sequence tags algorithms nucleic acid databases conserved sequence protein binding molecular sequence data mice dna sequence analysis systems integration humans plant gene expression regulation base sequence plant proteins plant dna plants gene regulatory networks protein sequence analysis proteins complementary dna database management systems amino acid sequence genes amino acid sequence homology genome binding sites oligonucleotide array sequence analysis triticum genetic models single nucleotide polymorphism lipids hordeum glucosyltransferases gene expression profiling photosynthesis ploidies plant chromosomes nucleic acid repetitive sequences genetic transcription retroelements nucleic acid sequence homology rna splice sites response elements initiator codon eukaryotic cells untranslated rna transcriptional regulatory elements polymerase chain reaction poaceae controlled vocabulary terminal repeat sequences saccharomyces cerevisiae gene components rats genetic polymorphism genetic markers fabaceae medline small interfering rna agricultural crops circadian rhythm dna primers rosaceae arabidopsis agamous protein reproducibility of results University of Toronto caenorhabditis elegans proteins caenorhabditis elegans bacterial proteins bacterial dna bacterial genome research genetics factual databases dehydration cold temperature genetic promoter regions plant diseases chromosome mapping chloroplast rna phylogeny ChIP-seq mitochondrial proteins mitochondrial genes chloroplasts cytidine dna dna-binding proteins rna editing rna tertiary protein structure