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Flymine Blog

Content

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
  • 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