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Content Sensors Based on Codon Structure and DNA Methylation for Gene Finding in Vertebrate Genomes

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Abstract

All vertebrate genomes are heavily methylated at CpG dinucleotide sites, and methylated CpG dinucleotides are prone to CpG→TpG mutations through spontaneous deamination. This leaves different footprints on coding and non-coding sequences. We capture these different fingerprints by five indices that can be used to discriminate between coding and non-coding (intron) sequences. We also show that a linear discriminant function derived from a training set of coding and intron sequences from human chromosome 22 can be successfully used in gene-finding of the zebrafish genome.

Key words

content sensor DNA methylation gene finding vertebrate genome codon structure 

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • X. Xia
    • 1
  1. 1.University of OttawaOttawaCanada

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