Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence

Abstract

We have developed a novel method for estimating the parameters of hidden Markov models for gene finding in newly sequenced species. Our approach does not rely on curated training data sets, but instead uses extrinsic evidence (including paired-end ditags that have not been used in gene finding previously) and iterative training. This new method is particularly suitable for annotation of species with large evolutionary distance to the closest annotated species. We have used our approach to produce an initial annotation of more than 16 000 genes in the newly sequenced Schistosoma japonicum draft genome. We established the high quality of our predictions by comparison to full-length cDNAs (withdrawn from the extrinsic evidence) and to CEGMA core genes. We also evaluated the effectiveness of the new training procedure on Caenorhabditis elegans genome. ExonHunter and the newest parametric files for S. japonicum genome are available for download at www.bioinformatics.uwaterloo.ca/downloads/exonhunter

The Schistosoma japonicum genome reveals features of host–parasite interplay

“…Protein encoding genes were predicted using ExonHunter 48 . The prediction program combined ab initio gene prediction with supporting evidence from S. japonicum and S. mansoni expressed sequence tags (ESTs), S. japonicum pair-end ditags (PETs), Swiss-Prot protein database 58 and protein domain database 59 .…”

Draft Genome Sequence of an Obligate Psychrophilic Yeast, Candida psychrophila NRRL Y-17665 T

“…To annotate the nuclear genome, protein-coding genes were predicted using ExonHunter ( 13 ) (with custom parameter training) and Augustus ( 14 ) (with model for Debaryomyces hansenii ). ExonHunter reported 5,827 protein-coding genes, and Augustus 5,502.…”

Schistosomiasis in the People's Republic of China: the Era of the Three Gorges Dam

“…The landmark availability of the complete sequences of the S. japonicum (171) and S. mansoni (18) genomes will provide the necessary ancillary information. As well, new approaches in antigen discovery through the generation of a large schistosome transcriptome database, gene finding, and the explosion in postgenome technologies, including DNA microarray profiling, proteomics, glycomics, immunomics, and the application of RNA interference (RNAi) and novel imaging techniques (2,24,25,41,53,72,73,75,76,85,95,109,126,127,179,189,197,205,219,224,230), provide an unprecedented opportunity to identify a new generation of vaccine target molecules that may induce greater potency than the current candidate schistosome antigens (138).…”