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1.  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations 
Nucleic Acids Research  2014;43(Database issue):D690-D697.
Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase ( and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.
PMCID: PMC4383921  PMID: 25398896
2.  Incidence, prevalence, and hybrid approaches to calculating disability-adjusted life years 
When disability-adjusted life years are used to measure the burden of disease on a population in a time interval, they can be calculated in several different ways: from an incidence, pure prevalence, or hybrid perspective. I show that these calculation methods are not equivalent and discuss some of the formal difficulties each method faces. I show that if we don’t discount the value of future health, there is a sense in which the choice of calculation method is a mere question of accounting. Such questions can be important, but they don’t raise deep theoretical concerns. If we do discount, however, choice of calculation method can change the relative burden attributed to different conditions over time. I conclude by recommending that studies involving disability-adjusted life years be explicit in noting what calculation method is being employed and in explaining why that calculation method has been chosen.
PMCID: PMC3462112  PMID: 22967055
Disability-adjusted life years; Incidence perspective; Prevalence perspective; Burden of disease; Discounting
3.  FlyBase: enhancing Drosophila Gene Ontology annotations 
Nucleic Acids Research  2008;37(Database issue):D555-D559.
FlyBase ( is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project—a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species.
PMCID: PMC2686450  PMID: 18948289
4.  Annotation of the Drosophila melanogaster euchromatic genome: a systematic review 
Genome Biology  2002;3(12):research0083.1-83.22.
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences.
Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes.
Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
PMCID: PMC151185  PMID: 12537572

Results 1-4 (4)