Software Trapping: A Strategy for Finding Genes in Large
Genomic Regions
Alexander Kamb, Chunwei Wang, Alun Thomas, Bradley S. DeHoff,
Franklin H. Norris, Katherine Richardson, Jasper Rine, Mark H.
Skolnick, Paul R. Rosteck Jr.
Myriad Genetics, Inc., 390 Wakara Way, Salt Lake City, Utah 84108; Lilly
Research Laboratories, Eli Lilly and Company, Lilly Corporate Center,
Indianapolis, Indiana 46285; Deparment of Molecular and Cellular Biology,
Division of Genetics, University of California, Berkeley, California 94720; and
Department of Medical Informatics, University of Utah, Salt Lake City, Utah
84132
Computers and Biomedical Research, 28(2):140-153 (1995)
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.
