Nucleic Acids Research, 2003, Vol. 31, No. 24 7271-7279
© 2003 Oxford University Press
Article |
Gene structure prediction in syntenic DNA segments
1 Molecular Biology Institute, 2 Molecular, Cell and Developmental Biology and 3 Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
*To whom correspondence should be addressed at 242 Boyer Hall, UCLA, 611 East CE Young Drive, Box 951570, Los Angeles, CA 90095, USA. Tel: +1 310 825 2546; Fax: +1 310 206 7286; Email: lake@mbi.ucla.edu
Present address:
Jonathan E. Moore, Biology Department, Pomona College, Claremont, CA 91711, USA
The accurate prediction of higher eukaryotic gene structures and regulatory elements directly from genomic sequences is an important early step in the understanding of newly assembled contigs and finished genomes. As more new genomes are sequenced, comparative approaches are becoming increasingly practical and valuable for predicting genes and regulatory elements. We demonstrate the effectiveness of a comparative method called pattern filtering; it utilizes synteny between two or more genomic segments for the annotation of genomic sequences. Pattern filtering optimally detects the signatures of conserved functional elements despite the stochastic noise inherent in evolutionary processes, allowing more accurate annotation of gene models. We anticipate that pattern filtering will facilitate sequence annotation and the discovery of new functional elements by the genetics and genomics communities.