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Murphy, T. (2014.1.17). Gnomon runs for Drosophila species. 
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FBrf0224144
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Personal communication to FlyBase
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Here are the Gnomon annotation runs for Drosophila species:
ftp://ftp.ncbi.nih.gov/pub/murphyte/.annotations_for_flybase/
I included the D. grimshawi dataset for posterity, but my inclination is to not use it. There is no RNA-seq data available and I think the annotation changes are a wash overall.
D. willistoni has 257M reads, but they're all short (37-50 mers) so our alignment process found the fewest number of filtered introns (39k), compared to 66-71k for most of the others. I think it's still an improvement compared to the old GLEAN set, but it would benefit from more data.
For some others, we used cross-species RNA-seq data with some tuning of alignment parameters. The results look fine, but same-species data would have helped:
D. persimilis -- no same-species data, used D. pseudoobscura RNA-seq
D. erecta -- no same-species data, used D. yakuba RNA-seq
D. sechellia -- little same-species data, complemented with D. simulans RNA-seq
Terence Murphy
NCBI
DOI
Related Publication(s)
FlyBase analysis

Changes affecting gene model number or type in release 1.04 of the annotated D.ananassae genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.04 of the annotated D.ananassae genome due to Gnomon gene prediction runs. [FBrf0227294]

Changes affecting gene model number or type in release 3.03 of the annotated D.pseudoobscura genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 3.03 of the annotated D.pseudoobscura genome due to Gnomon gene prediction runs. [FBrf0227295]

Changes affecting gene model number or type in release 2.01 of the annotated D.simulans genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 2.01 of the annotated D.simulans genome due to Gnomon gene prediction runs. [FBrf0227296]

Changes affecting gene model number or type in release 1.04 of the annotated D.yakuba genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.04 of the annotated D.yakuba genome due to Gnomon gene prediction runs. [FBrf0227297]

Changes affecting gene model number or type in release 1.04 of the annotated D.erecta genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.04 of the annotated D.erecta genome due to Gnomon gene prediction runs. [FBrf0227298]

Changes affecting gene model number or type in release 1.04 of the annotated D.willistoni genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.04 of the annotated D.willistoni genome due to Gnomon gene prediction runs. [FBrf0227407]

Changes affecting gene model number or type in release 1.04 of the annotated D.mojavensis genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.04 of the annotated D.mojavensis genome due to Gnomon gene prediction runs. [FBrf0227408]

Changes affecting gene model number or type in release 1.03 of the annotated D.virilis genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015-, Changes affecting gene model number or type in release 1.03 of the annotated D.virilis genome due to Gnomon gene prediction runs. [FBrf0227409]

Changes affecting gene model number or type in release 1.05 of the annotated D.ananassae genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2016, Changes affecting gene model number or type in release 1.05 of the annotated D.ananassae genome due to Gnomon gene prediction runs. [FBrf0230167]

Changes affecting gene model number or type in release 1.05 of the annotated D.erecta genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2016, Changes affecting gene model number or type in release 1.05 of the annotated D.erecta genome due to Gnomon gene prediction runs. [FBrf0230168]

Changes affecting gene model number or type in release 1.04 of the annotated D.virilis genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.04 of the annotated D.virilis genome due to Gnomon gene prediction runs. [FBrf0230169]

Changes affecting gene model number or type in release 1.05 of the annotated D.virilis genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2016, Changes affecting gene model number or type in release 1.05 of the annotated D.virilis genome due to Gnomon gene prediction runs. [FBrf0230170]

Changes affecting gene model number or type in release 1.05 of the annotated D.willistoni genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.05 of the annotated D.willistoni genome due to Gnomon gene prediction runs. [FBrf0230171]

Changes affecting gene model number or type in release 1.05 of the annotated D.yakuba genome due to Gnomon gene prediction runs.
FlyBase Consortium, 2015, Changes affecting gene model number or type in release 1.05 of the annotated D.yakuba genome due to Gnomon gene prediction runs. [FBrf0230172]

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