title: Software trapping: a strategy for finding genes in large genomic regions.
abstract: We present an approach to the gene identification phase of positional cloning that combines sparse sampling of DNA sequences from large genomic regions with computational analysis. We call the method "software trapping." The goal is to find coding exons while avoiding massive DNA sequence determination and contig assembly. Instead, rapid sequence sampling is combined with exon screening software such as a newly developed package called XPOUND to identify coding sequences. We have tested the approach using a set of model genomic sequences with known intron/exon structures as well as with bona fide P1 genomic clones. The results suggest that the strategy is a useful complement to other methods for finding genes in poorly characterized regions of genomes.
authors.affiliation: Myriad Genetics, Inc., Salt Lake City, Utah 84108, USA.
authors.forename: A
authors.initials: A
authors.lastname: Kamb
authors.forename: C
authors.initials: C
authors.lastname: Wang
authors.forename: A
authors.initials: A
authors.lastname: Thomas
authors.forename: B S
authors.initials: BS
authors.lastname: DeHoff
authors.forename: F H
authors.initials: FH
authors.lastname: Norris
authors.forename: K
authors.initials: K
authors.lastname: Richardson
authors.forename: J
authors.initials: J
authors.lastname: Rine
authors.forename: M H
authors.initials: MH
authors.lastname: Skolnick
authors.forename: P R
authors.initials: PR
authors.lastname: Rosteck
mesh_terms: D017101:Bacteriophage P1 / Q000235:genetics; D003001:Cloning, Molecular; D004279:DNA, Viral / Q000235:genetics; D005069:Evaluation Studies as Topic; D005091:Exons; D005821:Genetic Techniques / Q000706:statistics & numerical data; D016678:Genome; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D004279:DNA, Viral