Brona Brejova, Tomas Vinar, Yangyi Chen, Shengyue Wang, Guoping Zhao, Daniel G. Brown, Ming Li, Yan Zhou. Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence. Nucleic Acids Research, 37(7):e52. 2009.

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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quality of our predictions by comparison to full-length cDNAs (withdrawn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