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General Resources

The resources listed here include tools and databases for general information on a variety of model organisms.

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Found 30 links

Displaying 15 links

A Quick Guide To Sequenced GenomesResource Content

http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.sht...

Model Organisms > General Resources

The Quick Guide includes descriptions of more than 150 organisms and has links to sequencing centers and scientific abstracts.

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Codon Usage DatabaseDatabase Content

http://www.kazusa.or.jp/codon/

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.

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tagscodon factual databases

CodonOTool Content

http://digbio.missouri.edu/software/index.html

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

NAR Web Server Issue 2007
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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

dbESTDatabase Content

http://www.ncbi.nlm.nih.gov/dbEST/index.html

Model Organisms > General Resources

Expressed Sequence Tags database; a division of GenBank containing single-pass cDNA sequence reads

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DOE Joint Genome Institute Genome PortalDatabase Content

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

Model Organisms > Fish
Model Organisms > General Resources
Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Plants

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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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

Entrez GenomesDatabase Content

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

Model Organisms > General Resources

List of prominent complete genomes with access to BLAST and precomputed conserved domains and protein homologs in complete genome context.

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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

GCUA: Graphical Codon Usage AnalyserTool Content

http://gcua.schoedl.de

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

Graphical representation of codon bias

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Gene Set BuilderTool Content

http://www.cisreg.ca/gsb/

DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Human Genome > Other Resources
Model Organisms > General Resources
Protein > Sequence Retrieval

Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences.

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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages

Genome Centres and DatabasesResource Content

http://www.ncbi.nlm.nih.gov/genomes/static/links.html

DNA > Mapping and Assembly
Human Genome > Other Resources
Model Organisms > General Resources

Genome centers and databases listed by organism.

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GOLDDatabase Content

http://www.genomesonline.org/

DNA > Databases
Model Organisms > Databases
Model Organisms > General Resources

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. GOLD is in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification.

NAR Database Issue 2010
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tagsanimals archaeal genome bacterial genome computational biology genetic databases genome genomics humans nucleic acid databases protein databases tertiary protein structure

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

Intergr8Tool Content

http://www.ebi.ac.uk/integr8/

Human Genome > Other Resources
Model Organisms > General Resources

Integr8 is a browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO.

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tagsarchaeal dna bacterial dna genetic databases genomics proteomics systems integration

InterProScanTool Content

http://www.ebi.ac.uk/InterProScan/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Protein > Annotation and Function
Protein > Domains and Motifs

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

NAR Web Server Issue 2005
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tagsdatabase management systems dna sequence analysis humans protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

Tags associated with subcategory 'Model Organisms/General Resources'

humans animals genetic databases genomics genome computational biology database management systems protein databases factual databases systems integration algorithms mice sequence alignment proteins species specificity bacterial genome caenorhabditis elegans dna sequence analysis gene expression base sequence arabidopsis bacterial dna archaeal genome pseudomonas aeruginosa archaeal dna escherichia coli recombinant proteins phylogeny programming languages nucleic acid conformation plant genome oligonucleotide probes oligonucleotide array sequence analysis thermodynamics automated pattern recognition gene expression regulation fungal genes eukaryotic cells chromosome mapping conserved sequence information dissemination protein sequence analysis nucleic acid sequence homology molecular sequence data human genome project expressed sequence tags genes caenorhabditis contig mapping plant dna oryza sativa molecular cloning dna fingerprinting helminth dna dna genetic models national library of medicine (u.s.) national institutes of health (u.s.) National Center for Biotechnology Information (NCBI) tertiary protein structure genetic transcription research support as topic single nucleotide polymorphism gc rich sequence genetic code computer simulation codon united states base composition gene expression profiling rats transcriptional regulatory elements genetic linkage bioterrorism biomedical research helminth genome controlled vocabulary documentation genotype bacterial genes chemical dictionaries archaeal genes anti-infective agents amino acid sequence amino acid sequence homology biology arabidopsis proteins genetic variation invertebrates genetic polymorphism fungal genome cattle dogs nucleic acid regulatory sequences reference standards classification amino acid motifs natural language processing helminth genes rna synteny