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Links tagged with 'caenorhabditis elegans'

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Found 24 links

Displaying 15 links

COGsTool Content

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

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

CompareProspectorTool Content

http://compareprospector.stanford.edu/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

NAR Web Server Issue 2004
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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

DAnCERDatabase Content

http://wodaklab.org/dancer/

DNA > Databases

The DAnCER (Disease Annotated Chromatin Epigenetic Resource) resource integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks.

NAR Database Issue 2011
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tagsanimals caenorhabditis elegans chromatin disease drosophila melanogaster epigenomics genetic databases humans mice molecular sequence annotation protein conformation protein interaction mapping saccharomyces cerevisiae

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

ENDEAVOURTool Content

http://www.esat.kuleuven.be/endeavour

Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases.

This content is being maintained by ltranche.

NAR Web Server Issue 2008
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tagsalgorithms animal models animals caenorhabditis elegans cell differentiation chromosome mapping computational biology drosophila melanogaster gene expression regulation genes genetic models genetic predisposition to disease humans mice rats roc curve sensitivity and specificity statistical models zebrafish

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

GenePath2Tool Content

http://www.genepath.org/genepath2

Protein > Interactions, Pathways, Enzymes

GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.

NAR Web Server Issue 2005
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tagsanimals artificial intelligence caenorhabditis elegans computational biology dictyostelium dna dna mutational analysis dna sequence analysis expert systems gene expression regulation genes genetic epistasis genetic models genomics humans knowledge larva mutation neural networks (computer) research single-blind method

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

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

IsoBaseDatabase Content

http://isobase.csail.mit.edu/

Model Organisms > Databases
Protein > Databases

IsoBase is a database identifying functionally related proteins across five major eukaryotic model organisms: yeast, fly, worm, mouse, and human. Clusters were computed using the IsoRankN algorithm, which uses spectral methods, to combine sequence and PPI data to produce clusters of functionally related proteins. IsoBase may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword.

This content is being maintained by dkp.

NAR Database Issue 2011
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tagscaenorhabditis elegans cluster analysis drosophila melanogaster graph isomorphism graph spectral clustering humans interaction networks mice network alignment ortholog databases protein-protein interactions saccharomyces cerevisiae

JCatTool Content

http://www.jcat.de/

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

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

NAR Web Server Issue 2005
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tagsalgorithms animals caenorhabditis elegans codon escherichia coli gene expression pseudomonas aeruginosa recombinant proteins species specificity

mGene.webTool Content

http://www.mgene.org/web

DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

NAR Web Server Issue 2009
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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2003NAR Web Server Issue 2006NAR Web Server Issue 2007
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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

oPOSSUMTool Content

http://www.cisreg.ca/oPOSSUM_new/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.

NAR Web Server Issue 2007
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tagsalgorithms animals binding sites caenorhabditis elegans computational biology gene expression profiling gene expression regulation genetic promoter regions humans mice nf-kappa b nucleic acid databases oligonucleotide array sequence analysis saccharomyces cerevisiae transcription factors