Simplified Matching Algorithm Using a Translated Codon (Tron)
Vol. 16 no. 3 2000 BIOINFORMATICS Pages 190–202 Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps Osamu Gotoh Saitama Cancer Center Research Institute, 818 Komuro Ina-machi, Saitama 362-0806, Japan Received on August 23, 1999; accepted on October 21, 1999 Abstract Introduction Motivation: Locating protein-coding exons (CDSs) on a Following the completion of genomic sequencing of the eukaryotic genomic DNA sequence is the initial and an yeast Saccharomyces cerevisiae (Goffeau et al., 1996), essential step in predicting the functions of the genes nearly the complete structure of the nematode Caenorhab- embedded in that part of the genome. Accurate prediction ditis elegans genome has recently been reported (The of CDSs may be achieved by directly matching the DNA C. elegans Sequencing Consortium, 1998). Sequencing sequence with a known protein sequence or profile of a projects in several eukaryotic genomes including the homologous family member(s). human genome are now in progress. Identification of the Results: A new convention for encoding a DNA sequence genes on these genomic sequences and inferring their into a series of 23 possible letters (translated codon or functions are major themes of current computational tron code) was devised to improve this type of analysis. genome analyses. One obstacle to gene identification Using this convention, a dynamic programming algorithm is the fact that typical eukaryotic genes are segmented, was developed to align a DNA sequence and a protein and the prediction of precise exonic regions is still a sequence or profile so that the spliced and translated challenging problem (Burge and Karlin, 1998; Claverie, sequence optimally matches the reference the same as 1997; Murakami and Takagi, 1998).
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