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Links tagged with 'drosophila proteins'

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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

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

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

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

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

jPREdictorTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.

NAR Web Server Issue 2006
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tagsanimals binding sites drosophila melanogaster drosophila proteins genomics response elements transcription factors transcriptional regulatory elements

PhyloDomeTool Content

http://mendel.imp.univie.ac.at/PhyloDome/

Protein > Domains and Motifs
Protein > Phylogeny Reconstruction

PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.

NAR Web Server Issue 2005
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tagsanimals caenorhabditis elegans caenorhabditis elegans proteins drosophila proteins eukaryotic cells phylogeny protein sequence analysis proteins signal transduction tertiary protein structure

RBPDBDatabase Content

http://rbpdb.ccbr.utoronto.ca/

RNA > Databases

The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites.

NAR Database Issue 2011
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tagsanimals binding sites caenorhabditis elegans proteins drosophila proteins humans messenger rna mice protein databases rna sequence analysis rna-binding proteins tertiary protein structure
setsUniversity of Toronto

REDflyDatabase Content

http://redfly.ccr.buffalo.edu/?content=/search.php

Expression > Gene Regulation
Model Organisms > Fly

Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA sequence, their associated genes, and the expression patterns they direct.

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tagsanimals binding sites drosophila melanogaster drosophila proteins genetic databases genetic enhancer elements genomics online systems synteny systems integration transcription factors transcriptional regulatory elements

REDflyDatabase Content

http://redfly.ccr.buffalo.edu

Model Organisms > Databases

The REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both causal and power users and is intended as a tool for facilitating computational as well as experimental studies of transcriptional regulation.

This content is being maintained by halfon.

NAR Database Issue 2011
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tagsanimals binding sites drosophila melanogaster drosophila proteins genetic databases genetic enhancer elements genomics online systems synteny systems integration transcription factors transcriptional regulatory elements

TRANSFACDatabase Content

http://www.gene-regulation.com/pub/databases.html#transfac

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

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tagsanimals arabidopsis arabidopsis proteins binding sites database management systems developmental gene expression regulation dna dna-binding proteins drosophila melanogaster drosophila proteins eukaryotic cells factual databases gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans mice nucleic acid regulatory sequences rats saccharomyces systems integration tertiary protein structure tissue distribution transcription factors