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Worm

This section contains links to genome resources and databases for worms including the nematode, C. elegans.

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C. elegans Gene Knockout ConsortiumResource Content

http://www.celeganskoconsortium.omrf.org/

Model Organisms > Worm

Worldwide consortium whose ultimate goal is to produce null alleles of all known genes in the C. elegans genome; submit your gene to the knockout list.

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DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

Ensembl C.elegans Genome BrowserDatabase Content

http://www.ensembl.org/Caenorhabditis_elegans/

Model Organisms > Worm

Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl\'s comparative genomics resources.

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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

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.

NAR Web Server Issue 2010
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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

Interolog/Regulog DatabaseDatabase Content

http://interolog.gersteinlab.org/

Model Organisms > Fly
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast
Protein > Interactions, Pathways, Enzymes

Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

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tagsamino acid sequence amino acid sequence homology animals bacterial dna bacterial genome bacterial proteins binding sites caenorhabditis elegans caenorhabditis elegans proteins computational biology conserved sequence dna dna-binding proteins drosophila melanogaster drosophila proteins fungal dna fungal genome genome helicobacter pylori helminth dna protein binding protein databases protein interaction mapping proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins

TIGR Gene IndicesTool Content

http://compbio.dfci.harvard.edu/tgi/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Fish
Model Organisms > Fly
Model Organisms > General Resources
Model Organisms > Mouse and Rat
Model Organisms > Other Organisms
Model Organisms > Other Vertebrates
Model Organisms > Worm

An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.

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tagsanimals base sequence database management systems dna expressed sequence tags factual databases genes human genome project humans molecular sequence data nucleic acid sequence homology sequence alignment species specificity

UCSC C. briggsae Genome Browser GatewayTool Content

http://genome.ucsc.edu/cgi-bin/hgGateway?org=C.+briggsae&db=0&hgsid=27736277

Model Organisms > Worm

Provides a rapid and reliable display of any requested portion of the C. briggsae genome at any scale, together with dozens of aligned annotation tracks.

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tagsanimals california database management systems genetic databases genomics human genome humans mice

UCSC C. elegans Genome Browser GatewayTool Content

http://genome.ucsc.edu/cgi-bin/hgGateway?org=C.+elegans&db=0&hgsid=27736277

Model Organisms > Worm

Provides a rapid and reliable display of any requested portion of the C. elegans genome at any scale, together with dozens of aligned annotation tracks.

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tagsanimals california database management systems genetic databases genomics human genome humans mice

WormBaseDatabase Content

http://www.wormbase.org/

Model Organisms > Worm

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

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tagsanimals caenorhabditis caenorhabditis elegans data collection expressed sequence tags gene expression genomics helminth dna helminth rna neurons nucleic acid databases nucleic acid sequence homology rna interference single nucleotide polymorphism

WormBaseDatabase Content

http://www.wormbase.org

Model Organisms > Databases
Model Organisms > Worm

WormBase is a data repository for nematode biology. WormBase has expanded to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes.

NAR Database Issue 2010
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tagsalleles animals caenorhabditis caenorhabditis elegans computational biology genetic databases nucleic acid databases phenotype protein databases tertiary protein structure transcription factors

Tags associated with subcategory 'Model Organisms/Worm'

animals humans computational biology genomics genetic databases database management systems protein databases caenorhabditis elegans bacterial genome genome molecular sequence data sequence alignment helminth dna expressed sequence tags mice human genome factual databases proteins amino acid sequence homology base sequence algorithms phylogeny plant genome plant dna protein biosynthesis binding sites software design saccharomyces cerevisiae bacterial proteins parasites spirurida drosophila melanogaster genetic variation gene expression profiling dna-binding proteins helminth genes nematoda molecular evolution horizontal gene transfer tertiary protein structure saccharomyces cerevisiae proteins genes arabidopsis dna human genome project amino acid motifs gene regulatory networks nucleic acid sequence homology alleles artificial intelligence phenotype micrornas messenger rna gene expression regulation rna sequence analysis california transcription factors University of Toronto bacterial dna drosophila proteins drosophila protein conformation probability peptides proteome secondary protein structure caenorhabditis ubiquitin sequence analysis open reading frames molecular models anti-infective agents protein interaction mapping amino acid sequence archaeal genes archaeal genome initiator codon chemical dictionaries bacterial genes data collection gene expression caenorhabditis elegans proteins fungal genome benchmarking chromosome mapping codon dna sequence analysis conserved sequence fungal dna species specificity base composition nucleic acid databases neurons helminth rna rna interference single nucleotide polymorphism helicobacter pylori systems integration protein binding