http://bioinformatics.ca/links_directory/tag/drosophila-proteinshttp://bioinformatics.ca/links_directory/tag/drosophila-proteins/feed en http://www.cs.utoronto.ca/~juris/data/rnsc/Restricted Neighborhood Search Clustering Algorithm (RNSC): efficiently partitions networks into clusters using a cost function. Used to detect known and predict still undiscovered protein complexes within the cell's protein-protein interaction (PPI) network. The increasing amount of available PPI data necessitates an accurate and scalable approach to protein complex identification.13405Fri, 24 May 2013 19:50:36 -0400 http://www.moseslab.csb.utoronto.ca/alan/cis_reg_test.htmlStatistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.13380Thu, 23 May 2013 08:20:15 -0400 http://www.webscipio.orgScipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.13230Fri, 24 May 2013 08:20:18 -0400 http://gmod.org/wiki/GbrowseGBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.12640Thu, 23 May 2013 04:10:08 -0400 http://redfly.ccr.buffalo.eduThe 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.11901Thu, 23 May 2013 08:40:28 -0400 http://rbpdb.ccbr.utoronto.ca/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.11879Fri, 24 May 2013 12:40:16 -0400 http://droidb.org/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.11877Sat, 25 May 2013 08:40:32 -0400 http://pgfe.umassmed.edu/TFDBS/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.11782Fri, 24 May 2013 21:00:35 -0400 http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.htmlFlyTF 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.11687Thu, 23 May 2013 07:50:36 -0400 http://redfly.ccr.buffalo.edu/?content=/search.phpRegulatory 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.11440Thu, 23 May 2013 13:10:40 -0400 http://interolog.gersteinlab.org/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.11414Sat, 25 May 2013 17:10:26 -0400 http://genomebiology.com/series/drosophilaA series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.11237Thu, 23 May 2013 13:20:21 -0400 http://www.nematodes.org/nembase4/NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design. 10082Fri, 24 May 2013 23:40:44 -0400 http://e-rnai.dkfz.de/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.10049Fri, 24 May 2013 20:00:23 -0400 http://mendel.imp.univie.ac.at/PhyloDome/PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.9965Fri, 24 May 2013 20:40:24 -0400