Resources

• Tools
  • SRS Tools at the EBI
  • GBrowse – GBrowse genome browser
  • BLAST at the NCBI – Basic Local Alignment Search Tool to find regions of local similarity between sequences
  • Genotator – Sequence annotation
  • Genie – Gene finder
  • Promoter Prediction - A neural network based program to find possible transcription promoters
  • McPromoter – Promoter prediction for eukaryotes
  • Splice Site Prediction – Find possible 5′ and 3′ splice sites
  • SignalP - Signal peptide prediction
  • cis-analyst – Search for clusters of transcription factor binding sites
  • AHAB – Detection of enhancers and clusters of transcription factor binding sites in the genomes of multicellular organisms
  • Target Explorer – Search for clusters of transcription factor binding sites
  • Stubb – Search for clusters of cis-regulatory binding sites
  • Jmol – Jmol structural protein viewer
• Generic Databases
  • NCBI – National Center for Biotechnology Information
  • Ensembl – Automatic annotation on selected eukaryotic genomes
  • Harvester – Bioinformatic meta search engine for genes and protein associated information
  • SMART – Simple Modular Architecture Research Tool for the study of genetically mobile domains
  • Biozon – Biological database that integrates heterogenous data
  • GO – The Gene Ontology
  • SO – The Sequence Ontology
  • PubMed - Archive of life sciences journal literature
• Organism-specific/related Databases
  • BDGP – Berkeley Drosophila Genome Project
  • FlyBase - A database of the Drosophila genome
  • Interactive Fly - Guide to Drosophila development and metazoan evolution
  • DrosDel – An isogenic deficiency kit for Drosophila melanogaster
  • DPDB – Drosophila Polymorphism Database
  • FLIGHT – Integrating genomic and high-throughput data
  • FlyExpress – Image-matching search engine to find biologically similar gene expression patterns
  • FlyEx – A database of segmentation gene expression in Drosophila
  • VectorBase – database of vector-related data
  • Wormbase – A database concerning the genetics, genomics and biology of C. elegans and some related nematodes
  • euGenes – Genomic information for eukaryotic organisms
  • inParanoid – Eukaryotic ortholog groups
  • Homophila – Human disease to Drosophila gene database
• Protein Databases
  • BIND – Biomolecular Interaction Database
  • DIP – Database Interacting Proteins
  • IntAct – Protein interaction data
  • BioGrid – General repository for interaction datasets
  • Negative Proteome Database – Proteome Comparison
  • Interpro - Database of protein families, domains and functional sites
  • PDB – Protein Data Bank
  • Pfam – Protein Family Database
  • PSI – Protein Standards Initiative
  • String – Search Tool for the Retrieval of Interacting Genes/Proteins
  • Uniprot - Universal Protein Resource
• Transcriptional Regulation Databases
  • Drosophila DNase I Footprint Database – A systematic genome annotation of transcription factor binding sites in Drosophila
  • FlyTF – Drosophila Transcription Factor Database
  • REDfly – Regulatory Element Database for Drosophila
  • ORegAnno – Open Regulatory Annotation
• RNAi and Cell-assay Databases
  • DRSC – Drosophila RNAi Screening Center
  • GenomeRNAi – Database of phenotypes obtained in RNAi experiments in cultured Drosophila cells
  • LIFEdb – Database for Localization, Interaction, Functional assays and Expression of Proteins
• Microarray Databases
  • ArrayExpress - Repository for microarray data
  • FlyChip – The UK Drosophila microarray facility
  • Heidelberg FlyArray – Heidelberg FlyArray expression project
  • INDAC – International Drosophila Array Consortium
  • MAGE – MicroArray and Gene Expression group
  • GEO – Gene Expression Omnibus
• Pathways
  • Biocarta pathways – Proteomic pathway project
  • KEGG pathway database - Wiring diagrams of molecular interactions, reactions, and relations
  • Reactome – A curated knowledgebase of biological pathways
  • Wnt pathways – A database on Wnt signaling