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Updated: Aug 30, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
A novel index which precisely derives protein coding regions from cross-species genome alignments
Hideki Noguchi1, Tetsushi Yada, Yoshiyuki Sakaki
1Genomic Sciences Center, RIKEN, 1-7-22 Furo-cho, Tsurumi-ku, Yokohama 230-0045, Japan. hide@gsc.riken.go.jp
Abstract:
We introduce here a novel index which precisely derives protein coding regions from cross-species genome alignments. The index is deeply related to frame recovery observed in coding sequence alignments, that is, if insertions or deletions of nucleotides causes frame shifts in coding regions, other in-dels which recover the reading frames will be often observed in the vicinity. In contrast, such frame recoveries are not observed in other conserved regions. We prepared two gene models: a model which finds gene by using sequence similarity and intrinsic gene measures (basic model), and the other model which finds gene by using frame recovery index in addition to sequence similarity and intrinsic gene measures (frame recovery model). We evaluated the prediction accuracies of the two models, and our benchmark test revealed that frame recovery model significantly improved the prediction accuracy in comparison with basic model.
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