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Links tagged with 'plant genome'

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Found 32 links

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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

deepBaseDatabase Content

http://deepbase.sysu.edu.cn/

RNA > Databases

deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. deepBase facilitates the comprehensive annotation and discovery of small RNAs from transcriptomic data such as ncRNA-associated small RNAs (nasRNAs), promoter-associated small RNAs (pasRNAs), exon-associated small RNAs (easRNAs), repeat-associated small RNAs (rasRNAs) and miRNA and snoRNA candidates. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display.

NAR Database Issue 2010
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tagsalgorithms animals computational biology gene expression profiling genetic databases humans nucleic acid databases plant genome protein databases rna sequence analysis sequence alignment

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

Ensembl GenomesDatabase Content

http://www.ensemblgenomes.org

Model Organisms > Databases

Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

NAR Database Issue 2010
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tagsanimals anopheles gambiae bacterial genome classification computational biology fungal genome gene expression genetic databases genetic polymorphism genome humans invertebrates nucleic acid databases open reading frames plant genome search engine single nucleotide polymorphism tertiary protein structure

GenBankDatabase Content

http://www.ncbi.nlm.nih.gov

DNA > Databases

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases.

NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms animals bacterial genome computational biology expressed sequence tags genetic databases genomics high-throughput nucleotide sequencing humans metagenomics molecular sequence annotation national institutes of health (u.s.) national library of medicine (u.s.) nucleic acid databases plant genome protein databases united states viral genome

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

Genome Database for RosaceaeDatabase Content

http://www.rosaceae.org/

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE
Model Organisms > Plants

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.

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tagschromosome mapping expressed sequence tags genetic databases genetic markers genetics genomics plant genome research rosaceae sequence alignment systems integration

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

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

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

MetaCycDatabase Content

http://metacyc.org/

Protein > Databases

The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.

NAR Database Issue 2010
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tagsanimals archaeal genome bacterial genome biological models computational biology genetic databases humans nucleic acid databases plant genome protein databases tertiary protein structure viral genome

MIPSDatabase Content

http://mips.helmholtz-muenchen.de

Protein > Databases

The Munich Information Center for Protein Sequences (MIPS) provides annotated collections of biological data. High-quality reference resources include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis.

NAR Database Issue 2011
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tagsdata mining genetic databases genomics metabolomics micrornas neoplasm genes phenotype plant genome protein databases protein sequence analysis proteomics systems integration

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