title: Genome-guided transcript assembly by integrative analysis of RNA sequence data.
abstract: The identification of full length transcripts entirely from short-read RNA sequencing data (RNA-seq) remains a challenge in the annotation of genomes. Here we describe an automated pipeline for genome annotation that integrates RNA-seq and gene-boundary data sets, which we call Generalized RNA Integration Tool, or GRIT. Applying GRIT to Drosophila melanogaster short-read RNA-seq, cap analysis of gene expression (CAGE) and poly(A)-site-seq data collected for the modENCODE project, we recovered the vast majority of previously annotated transcripts and doubled the total number of transcripts cataloged. We found that 20% of protein coding genes encode multiple protein-localization signals and that, in 20-d-old adult fly heads, genes with multiple polyadenylation sites are more common than genes with alternative splicing or alternative promoters. GRIT demonstrates 30% higher precision and recall than the most widely used transcript assembly tools. GRIT will facilitate the automated generation of high-quality genome annotations without the need for extensive manual annotation.
authors.affiliation: Department of Biostatistics, University of California at Berkeley, Berkeley, California, USA.
authors.forename: Nathan
authors.identifier: 0000000171142450
authors.initials: N
authors.lastname: Boley
authors.affiliation: Department of Biostatistics, University of California at Berkeley, Berkeley, California, USA.
authors.forename: Marcus H
authors.initials: MH
authors.lastname: Stoiber
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Benjamin W
authors.initials: BW
authors.lastname: Booth
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wan
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Hoskins
authors.affiliation: 1] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [2].
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bickel
authors.affiliation: 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2].
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.affiliation: 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [2] Department of Statistics, University of California at Berkeley, Berkeley, California, USA. [3].
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D004331:Drosophila melanogaster / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D012313:RNA / Q000032:analysis / Q000737:chemistry* / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA