title: Vertebrate gene predictions and the problem of large genes.
abstract: To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistently low false-negative rate. The incorporation of similarity information is meant to reduce the false-positive rate, but in doing so it increases the false-negative rate. The crucial variable is gene size (including introns)--genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted.
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: ShengTing
authors.initials: S
authors.lastname: Li
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: HongKun
authors.initials: H
authors.lastname: Zheng
authors.forename: Zhao
authors.initials: Z
authors.lastname: Xu
authors.forename: Jia
authors.initials: J
authors.lastname: Ye
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
mesh_terms: D000818:Animals; D005091:Exons; D015870:Gene Expression; D005821:Genetic Techniques / Q000706:statistics & numerical data; D015894:Genome, Human; D006801:Humans; D007438:Introns; D008957:Models, Genetic; D009928:Organ Specificity; D011237:Predictive Value of Tests; D014714:Vertebrates / Q000235:genetics*