Here is a collection of online databases and information that we find useful and relevant to our research. Whether we are looking for genomic tools to make transgenic flies or checking the latest publications on RNAi, these are some of the sites we visit regularly.
Useful Links
General Scientific Information
NCBI: National Center for Biotechnology Information database (PubMed, GenBank, BLAST…)
Gene Ontology: gene and gene product classification by function
KEGG: Kyoto Encyclopedia of Genes and Genomes
ExPASy: Bioinformatics resource portal of Swiss Institute of Bioinformatics
SRS@EBI: Sequence Retrieval System at European Bioinformatics Institute
Fly-Related Information
FlyBase: the Drosophila genes and genomes database
BestGene: the Drosophila embryo injection and transgenic service
Bloomington Drosophila Stock Center (flystocks) at Indiana University
Deletion Hunter: a tool to identify FRT site compatible for at will genomic deletion
Drosophila Genomics Resource Center (DGRC) at Indiana University
Drosophila Image Award by the Genetics Society of America
Drosophila Species Stock Center (DSSC) at University of California San Diego
Drosophila RNAi Screening Center (DRSC & TRiP) at Harvard Medical School
Exelixis Collection at Harvard Medical School
FlyAtlas: the Drosophila gene expression atlas (see the brand new search page FlyAtlas2)
FlyC31: the PhiC31 integrase system for Drosophila transgenics
FlyCRISPR: the powerful RNA-guided gene editing method applied to Drosophila
FlyMine: an integrated genomics database for Drosophila
FlyMove: an internet resource to study the development of the fruit fly
FlyORF: the UAS-ORF lines project at Zurich University
Fly RMCE: a resource to use the PhiC31-mediated Recombinase Mediated Cassette Exchange (RMCE)
Flyshop services at Duke University
Fly vectors #1: common cloning vectors and constructs used at Flybase
Fly vectors #2: common cloning vectors and constructs used at Utha University
Gateway Drosophila Vector Collection: a list of fly-compatible Gateway vectors at Paris 6 University
Gene Disruption Project (GDP): a database of non-targeted transposon mutagenized flies
The Interactive Fly: a cyberspace guide to Drosophila genes and their role in development (see the atlas)
Vienna Drosophila RNAi Center (VDRC): the Drosophila transgenic RNAi library
VectorBase: a genomic resource for the arthropod vector community
Molecular Biology
Primer3: online PCR primer design software (see also Primer3Plus interface)
OligoCalc: oligonucleotide properties calculator
OligoWalk: online server calculating thermodynamic features of siRNAs
Codon Usage: codon usage database from Kazusa DNA Research Institute
4Peaks: Mac OS X application for viewing and editing sequence trace files
ClustalW (KUBiC): multiple sequence alignment software at Kyoto University Bioinformatics Center
ClustalW (SIB): multiple sequence alignment software at Swiss Institute of Bioinformatics
ProteinMW: protein molecular weight calculator
Genscan: gene structure prediction
T-test: online t-test helper
Translate: online translation tool
mfold: RNA secondary structure prediction
E.coli Wiki: Escherichia coli genotypes
RNA Interference
Non-coding RNA: a set of recent Nature Reviews
RNA Interfercence Video and Slideshow: an animation available here (see the slideshow on Nature‘s website)
