Journal Article

Mapping Hidden Potential Identity Elements by Computing the Average Discriminating Power of Individual tRNA Positions

Áron Szenes and Gábor Pál

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 19, issue 3, pages 245-258
Published in print June 2012 | ISSN: 1340-2838
Published online February 2012 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dss008

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The recently published discrete mathematical method, extended consensus partition (ECP), identifies nucleotide types at each position that are strictly absent from a given sequence set, while occur in other sets. These are defined as discriminating elements (DEs). In this study using the ECP approach, we mapped potential hidden identity elements that discriminate the 20 different tRNA identities. We filtered the tDNA data set for the obligatory presence of well-established tRNA features, and then separately for each identity set, the presence of already experimentally identified strictly present identity elements. The analysis was performed on the three kingdoms of life. We determined the number of DE, e.g. the number of sets discriminated by the given position, for each tRNA position of each tRNA identity set. Then, from the positional DE numbers obtained from the 380 pairwise comparisons of the 20 identity sets, we calculated the average excluding value (AEV) for each tRNA position. The AEV provides a measure on the overall discriminating power of each position. Using a statistical analysis, we show that positional AEVs correlate with the number of already identified identity elements. Positions having high AEV but lacking published identity elements predict hitherto undiscovered tRNA identity elements.

Keywords: tRNA; identity element prediction; extended consensus partition

Journal Article.  8077 words.  Illustrated.

Subjects: Genetics and Genomics

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