Automated annotation of yeast genomes

Abstract

I have built an automated annotation pipeline (named YGAP - Yeast Genome Annotation Pipeline), designed specifically for new yeast genome sequences lacking transcriptome data. YGAP uses homology and synteny information from other yeast species stored in the Yeast Gene Order Browser (YGOB) database to annotate yeast genomes using the outputs from high-throughput sequencing methods. The pipeline is able to detect probable frameshift sequencing errors and can propose corrections for them. YGAP searches intelligently for introns, and detects tRNA genes and Ty-like elements. Using YGAP, I have automatically reannotated the genomes of Saccharomyces cerevisiae and Naumovozyma castellii, and compared the annotation results to those obtained with another popular annotation pipeline, AUGUSTUS. For S. cerevisiae and N. castellii, 91-93% of YGAP's predicted gene structures were identical to those in previous manually curated gene sets, and it outperforms AUGUSTUS.