An integrated computational pipeline and database to support whole-genome sequence annotation

CJ Mungall¹ , S Misra²^,3, BP Berman², J Carlson⁴, E Frise⁴, N Harris³^,4, B Marshall², S Shu²^,3, JS Kaminker²^,3, SE Prochnik²^,3, CD Smith²^,3, E Smith²^,3, JL Tupy²^,3, C Wiel²^,3, GM Rubin¹^,2^,3^,4 and SE Lewis²^,3

¹Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA

²Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720-3200, USA

³FlyBase-Berkeley, University of California, Berkeley, CA 94720-3200, USA

⁴Genome Sciences Department, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA

author email corresponding author email

Genome Biology 2002, 3:research0081.1-0081.11doi:10.1186/gb-2002-3-12-research0081


Published:	23 December 2002

This article is part of a series of refereed research articles from Berkeley Drosophila Genome Project, FlyBase and colleagues, describing Release 3 of the Drosophila genome, which are freely available at http://genomebiology.com/drosophila/.

Subject areas: Bioinformatics, Methods, Genome studies, Model organisms

Abstract

We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome annotation. The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture.