title: Gene recognition based on DAG shortest paths.
abstract: We describe DAGGER, an ab initio gene recognition program which combines the output of high dimensional signal sensors in an intuitive gene model based on directed acyclic graphs. In the first stage, candidate start, donor, acceptor, and stop sites are scored using the SNoW learning architecture. These sites are then used to generate a directed acyclic graph in which each source-sink path represents a possible gene structure. Training sequences are used to optimize an edge weighting function so that the shortest source-sink path maximizes exon-level prediction accuracy. Experimental evaluation of prediction accuracy on two benchmark data sets demonstrates that DAGGERis competitive with ab initio gene finding programs based on Hidden Markov Models.
authors.affiliation: Department of Computer Science, University of Illinois at Urbana-Champaign, Digital Computing Laboratory, Urbana, Illinois 61801, USA. jsc@ocf.berkeley.edu
authors.forename: J S
authors.initials: JS
authors.lastname: Chuang
authors.forename: D
authors.initials: D
authors.lastname: Roth
mesh_terms: D019295:Computational Biology; D004247:DNA / Q000235:genetics; D030561:Databases, Nucleic Acid; D005796:Genes; D005821:Genetic Techniques / Q000706:statistics & numerical data*; D012984:Software
chemical_list: D004247:DNA