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Links tagged with 'drosophila'

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DroIDDatabase Content

http://droidb.org/

DNA > Databases
Model Organisms > Databases
Protein > Databases

DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are annotated with experimental details and periodically updated confidence scores. The database now includes transcription factor-gene and regulatory RNA-gene interactions. Orthologous gene mappings of Drosophila genes to other organisms are also available to facilitate finding interactions based on gene names and identifiers for a number of common model organisms and humans.

NAR Database Issue 2011
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tagsanimals drosophila drosophila proteins gene expression gene regulatory networks genetic databases insect genes micrornas protein interaction mapping systems integration transcription factors

Drosophila DNase I footprint databaseDatabase Content

http://www.flyreg.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Fly

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

This content is being maintained by caseybergman.

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tagsbinding sites dna footprinting drosophila genome annotation transcription factors
setsUniversity of Manchester

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

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

FlyFactorSurveyDatabase Content

http://pgfe.umassmed.edu/TFDBS/

Model Organisms > Databases

FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices for TFs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome.

NAR Database Issue 2011
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tagsanimals bacteria binding sites drosophila drosophila proteins genetic databases transcription factors transcriptional regulatory elements two-hybrid system techniques

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

McPromoterTool Content

http://genes.mit.edu/McPromoter.html

DNA > Structure and Sequence Feature Detection

The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites.

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tagsanimals computational biology dna drosophila genetic models genetic promoter regions likelihood functions markov chains neural networks (computer) nucleic acid databases physical chemistry physicochemical phenomena statistical models stochastic processes

MKTTool Content

http://mkt.uab.es

DNA > Sequence Polymorphisms

Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.

NAR Web Server Issue 2008
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tagsanimals codon dna sequence analysis drosophila genetic selection genetic variation

PDATool Content

http://pda.uab.es/pda2/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Sequence Comparison > Analysis of Aligned Sequences

PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.

This content is being maintained by soniacas.

NAR Web Server Issue 2004NAR Web Server Issue 2006
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tagsalgorithms animals dna sequence analysis drosophila genetic polymorphism nucleic acid databases sequence alignment

RNAhybridTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Expression > Gene Regulation
RNA > Functional RNAs

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.

NAR Web Server Issue 2006
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tags3' untranslated regions algorithms animals binding sites body patterning caenorhabditis elegans caenorhabditis elegans proteins computational biology drosophila homeodomain proteins insect genes messenger rna micrornas nucleic acid conformation nucleic acid databases post-transcriptional rna processing rna interference thermodynamics

SAPS - Statistical Analysis of Protein SequencesTool Content

http://www.ebi.ac.uk/Tools/saps/

Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Calculations include compositional analysis, charge distribution, identification of highly hydrophobic (transmembrane) segments, sequence repeats, and more.

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tagsalgorithms amino acid sequence animals drosophila humans molecular sequence data nucleic acid sequence homology proteins proto-oncogene proteins c-myc

siDirectTool Content

http://design.RNAi.jp/

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.

NAR Web Server Issue 2004
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tagsalgorithms animals base sequence cell line chick embryo cricetinae drosophila gc rich sequence genetic models genetic vectors humans luciferases mammals mice molecular sequence data rna interference small interfering rna transfection

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques