Genome-guided transcript assembly by integrative analysis of RNA sequence data

Nat Biotechnol. 2014 Apr;32(4):341-6. doi: 10.1038/nbt.2850. Epub 2014 Mar 16.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Chromosome Mapping / methods*
  • Drosophila melanogaster / genetics
  • Genome, Insect / genetics
  • Genomics / methods*
  • Molecular Sequence Annotation / methods*
  • RNA / analysis
  • RNA / chemistry*
  • RNA / genetics*
  • Sequence Analysis, RNA / methods*


  • RNA

Associated data

  • SRA/SRR070420
  • SRA/SRR070421
  • SRA/SRR070424
  • SRA/SRR111882
  • SRA/SRR1151373
  • SRA/SRR1151374
  • SRA/SRR488279
  • SRA/SRR488280