Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

Jun Li¹ , Michelle M Riehle¹ , Yan Zhang¹ , Jiannong Xu¹ , Frederick Oduol¹ , Shawn M Gomez² , Karin Eiglmeier² , Beatrix M Ueberheide³ , Jeffrey Shabanowitz³ , Donald F Hunt³ , José MC Ribeiro⁴ and Kenneth D Vernick¹

¹Center for Microbial and Plant Genomics, and Department of Microbiology, University of Minnesota, St Paul, MN 55108, USA

²Unité de Biochimie et Biologie Moléculaire des Insectes and CNRS FRE 2849, Institut Pasteur, 75724 Paris Cedex 15, France

³Department of Chemistry, McCormick Rd, University of Virginia, Charlottesville, VA 22904, USA

⁴Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA

author email corresponding author email

Genome Biology 2006, 7:R24doi:10.1186/gb-2006-7-3-r24


Published:	27 March 2006

Subject areas: Bioinformatics, Genome studies, Model organisms

Abstract

Background

Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector.

Results

We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download.

Conclusion

Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms.