Release 8.0

In release 8.0 we have updated the data model for protein interactions, protein structure and orthologues to make them easier and faster to query. We also include three new data sets: Tiffin (predicted regulatory motifs), anoEST (A. gambiae EST clusters) and predicted 3-D protein structures for A. gambiae domains. A new type of constraint is used in template queries which now allows you to enter any identifier or symbol.

  • Data
    • NEW – D. melanogaster predicted regulatory motifs and functional sites (motif instances) from the Tiffin database. Note these have been mapped to the release 5.0 genome sequence.
    • NEW – A. gambiae EST and EST clusters from the Imperial College London Centre for Bioinformatics.
    • NEW – A. gambiae protein domain 3-D structure predictions from Kenji Mizuguchi. This data provides structure predictions for regions of A. gambiae proteins that correspond to a Pfam domain.
    • NEW – H. sapiens and M. musculus protein information included from UniProt, we already include InParanoid orthologues to these organisms.
  • User Interface
    • NEW – LOOKUP constraints. Most template queries are now updated to use a new type of constraint. Now you don’t need to enter a specific type of identifier – for example for the D. melanogaster gene zen you could enter ‘zen’, ‘CG1046’, ‘FBgn0004053’ or ‘zerknullt’ and get the same result. You could even enter a protein and or transcript identifier and it would find the gene.

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I make software & yarn things. Heart open*, scifi, cycling, running, veggies. 🇳🇿🇮🇱🇬🇧🇪🇺🏳️‍🌈. @yoyehudi on Twitter, but also @codeisscience & @intermineorg. @softwaresaved Fellow 2018.