Curated data sets for assessment

• Standard 3 (Adh.std3.gff) “more complete gene set”

  • 222 gene structures (39 single- and 183 multi- coding exon genes)
  • Criteria:
    • Annotated as described in Ashburner et al.
    • cDNA to genomic alignment using sim4
    • Start codons predicted by ORFFinder (Frise et al., unpublished)
    • ~182 genes have similarity to a homologous protein sequence in another organism or have a Drosophila EST hit
      • Edge verification by partial EST/cDNA alignments
      • BLASTX, TBLASTX homology results
      • PFAM alignments
      • Gene structure verification using GenScan (human)
    • 14 genes had EST/homology hits but no gene finding predictions
    • ~40 genes only have “strong” GenScan predictions

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