TOOLS and DATABASES
  • Tools
    • SRS Tools at the EBI - [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+applSelect]
    • GBrowse - GBrowse genome browser - [http://www.gmod.org/ggb/index.shtml]
    • BLAST at the NCBI - Basic Local Alignment Search Tool to find regions of local similarity between sequences - [http://www.ncbi.nih.gov/BLAST]
    • Genotator - Sequence annotation - [http://www.fruitfly.org/~nomi/genotator]
    • Genie - Gene finder - [http://www.fruitfly.org/seq_tools/genie.html]
    • Promoter Prediction - A neural network based program to find possible transcription promoters - [http://www.fruitfly.org/seq_tools/promoter.html]
    • McPromoter - Promoter prediction for eukaryotes - [http://genes.mit.edu/McPromoter.html]
    • Splice Site Prediction - Find possible 5' and 3' splice sites - [http://www.fruitfly.org/seq_tools/splice.html]
    • SignalP - Signal peptide prediction - [http://www.cbs.dtu.dk/services/SignalP]
    • cis-analyst - Search for clusters of transcription factor binding sites - [http://rana.lbl.gov/cis-analyst]
    • AHAB - Detection of enhancers and clusters of transcription factor binding sites in the genomes of multicellular organisms - [http://gaspard.bio.nyu.edu/Ahab.html]
    • Target Explorer - Search for clusters of transcription factor binding sites - [http://honiglab.cpmc.columbia.edu/Target_Explorer]
    • Stubb - Search for clusters of cis-regulatory binding sites - [http://stubb.rockefeller.edu]
    • Jmol - Jmol structural protein viewer - [http://jmol.sourceforge.net]
  • Generic Databases
    • NCBI - National Center for Biotechnology Information - [http://www.ncbi.nlm.nih.gov]
    • Ensembl - Automatic annotation on selected eukaryotic genomes - [http://www.ensembl.org]
    • Harvester - Bioinformatic meta search engine for genes and protein associated information - [http://harvester.embl.de]
    • SMART - Simple Modular Architecture Research Tool for the study of genetically mobile domains- [http://smart.embl-heidelberg.de]
    • Biozon - Biological database that integrates heterogenous data - [http://biozon.org]
    • GO - The Gene Ontology - [http://www.geneontology.org]
    • SO - The Sequence Ontology - [http://song.sourceforge.net]
    • PubMed - Archive of life sciences journal literature - [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed]
  • Organism-specific/related Databases
    • BDGP - Berkeley Drosophila Genome Project - [http://www.fruitfly.org]
    • FlyBase - A database of the Drosophila genome - [http://www.flybase.org]
    • Interactive Fly - Guide to Drosophila development and metazoan evolution - [http://interactive-fly]
    • DrosDel - An isogenic deficiency kit for Drosophila melanogaster - [http://www.drosdel.org.uk]
    • DPDB - Drosophila Polymorphism Database - [http://bioinformatica.uab.es/dpdb]
    • FLIGHT - Integrating genomic and high-throughput data - [http://flight.licr.org]
    • FlyExpress - Image-matching search engine to find biologically similar gene expression patterns - [http://www.flyexpress.net]
    • FlyEx - A database of segmentation gene expression in Drosophila - [http://flyex.ams.sunysb.edu/FlyEx]
    • VectorBase - database of vector-related data - [http://www.vectorbase.org]
    • Wormbase - A database concerning the genetics, genomics and biology of C. elegans and some related nematodes - [http://www.wormbase.org]
    • euGenes - Genomic information for eukaryotic organisms - [http://eugenes.org]
    • inParanoid - Eukaryotic ortholog groups - [http://inparanoid.cgb.ki.se]
    • Homophila - Human disease to Drosophila gene database - [http://superfly.ucsd.edu/homophila]
  • Protein Databases
    • BIND - Biomolecular Interaction Database - [http://www.bind.ca/Action]
    • DIP - Database Interacting Proteins - [http://dip.doe-mbi.ucla.edu]
    • IntAct - Protein interaction data - [http://www.ebi.ac.uk/intact]
    • BioGrid - General repository for interaction datasets - [http://www.thebiogrid.org]
    • Negative Proteome Database - Proteome Comparison - [http://superfly.ucsd.edu/negprot]
    • Interpro - Database of protein families, domains and functional sites - [http://www.ebi.ac.uk/interpro]
    • PDB - Protein Data Bank - [http://www.rcsb.org/pdb]
    • Pfam - Protein Family Database - [http://www.sanger.ac.uk/Software/Pfam]
    • PSI - Protein Standards Initiative - [http://psidev.sourceforge.net]
    • String - Search Tool for the Retrieval of Interacting Genes/Proteins - [http://string.embl-heidelberg.de]
    • Uniprot - Universal Protein Resource - [http://www.ebi.ac.uk/uniprot]
  • Transcriptional Regulation Databases
    • Drosophila DNase I Footprint Database - A systematic genome annotation of transcription factor binding sites in Drosophila - [http://www.flyreg.org]
    • FlyTF - Drosophila Transcription Factor Database - [http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF]
    • REDfly - Regulatory Element Database for Drosophila - [https://redfly.ccr.buffalo.edu]
    • ORegAnno - Open Regulatory Annotation - [http://www.oreganno.org]
  • RNAi and Cell-assay Databases
    • DRSC - Drosophila RNAi Screening Center - [http://flyrnai.org/RNAi_index.html]
    • GenomeRNAi - Database of phenotypes obtained in RNAi experiments in cultured Drosophila cells - [http://rnai.dkfz.de]
    • LIFEdb - Database for Localization, Interaction, Functional assays and Expression of Proteins - [http://www.dkfz.de/LIFEdb]
  • Microarray Databases
    • ArrayExpress - Repository for microarray data - [http://www.ebi.ac.uk/arrayexpress]
    • FlyChip - The UK Drosophila microarray facility - [http://www.flychip.org.uk]
    • Heidelberg FlyArray - Heidelberg FlyArray expression project - [http://hdflyarray.zmbh.uni-heidelberg.de]
    • INDAC - International Drosophila Array Consortium - [http://www.indac.net]
    • MAGE - MicroArray and Gene Expression group - [http://www.mged.org/Workgroups/MAGE/mage.html]
    • GEO - Gene Expression Omnibus - [http://www.ncbi.nlm.nih.gov/projects/geo]
  • Pathways
    • Biocarta pathways - Proteomic pathway project - [http://www.biocarta.com]
    • KEGG pathway database - Wiring diagrams of molecular interactions, reactions, and relations - [http://www.genome.jp/kegg/pathway.html]
    • Reactome - A curated knowledgebase of biological pathways - [http://www.reactome.org]
    • Wnt pathways - A database on Wnt signaling - [http://www.stanford.edu/~rnusse/wntwindow.html]