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Links tagged with 'drosophila melanogaster'

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Found 28 links

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AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

Berkeley Drosophila Genome ProjectResource Content

http://www.fruitfly.org/

Model Organisms > Fly

Good entrez to fly genome resources.

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tagsamino acid sequence animals base sequence cell line cluster analysis complementary dna dna sequence analysis drosophila melanogaster expressed sequence tags gene library genetic databases genome insect genes male membrane glycoproteins membrane proteins molecular sequence data rna sequence alignment testis

BSQATool Content

http://www.beespace.uiuc.edu/QuestionAnswer

Literature > Text Mining and Semantics
Model Organisms > Fly

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

NAR Web Server Issue 2010
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tagsanimal behavior animals data mining drosophila melanogaster gene expression regulation homeodomain proteins insect genes insects systems integration trans-activators

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

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

FlyBaseDatabase Content

http://flybase.bio.indiana.edu/

Model Organisms > Fly

FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.

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tagsanimals bibliography as topic california chromosome mapping computational biology drosophila drosophila melanogaster drosophila proteins europe factual databases gene expression gene library genetic databases genetic models genetic transcription genome insect genes mutation phenotype publishing research

FlyTFDatabase Content

http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html

Model Organisms > Databases

FlyTF is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.

NAR Database Issue 2010
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tagsanimals computational biology dna drosophila melanogaster drosophila proteins genetic databases genetic transcription nucleic acid databases protein databases tertiary protein structure transcription factors

GeneFizzTool Content

http://pbga.pasteur.fr/GeneFizz/

DNA > Gene Prediction

GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.

NAR Web Server Issue 2003
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tagsalgorithms animals biophysical phenomena biophysics computational biology dna dna sequence analysis drosophila melanogaster genes genetic code genetic models genetic techniques genomics molecular evolution nucleic acid conformation plasmodium falciparum protozoan dna protozoan genes protozoan genome

Genome SurveyorTool Content

http://veda.cs.uiuc.edu/gs

Expression > Gene Regulation
Model Organisms > Fly

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

NAR Web Server Issue 2011
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tagsanimals binding sites drosophila drosophila melanogaster insect genome transcription factors transcriptional regulatory elements

GenomeRNAiDatabase Content

http://rnai2.dkfz.de

Model Organisms > Databases

The GenomeRNAi database contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. GenomeRNAi also enables reporting of data from microscopy experiments and curated phenotypes from published screens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome. GenomeRNAi also facilitates the integration with other genomic data sets and contains expression profiling (RNA-Seq) data for several cell lines commonly used in RNAi experiments.

NAR Database Issue 2010
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tagsanimals cell line computational biology drosophila melanogaster genetic databases genomics humans nucleic acid databases nucleic acid probes protein databases rna interference tertiary protein structure

HMMgeneTool Content

http://genome.cbs.dtu.dk/services/HMMgene/

DNA > Gene Prediction

Prediction of vertebrate and C. elegans genes.

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tagsalcohol dehydrogenase animals computational biology computer-assisted numerical analysis drosophila melanogaster factual databases insect genes markov chains nucleic acid sequence homology sensitivity and specificity

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