Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russia.
DNA Res. 2019 Apr 1;26(2):157-170. doi: 10.1093/dnares/dsy046.
A new mathematical method for potential reading frameshift detection in protein-coding sequences (cds) was developed. The algorithm is adjusted to the triplet periodicity of each analysed sequence using dynamic programming and a genetic algorithm. This does not require any preliminary training. Using the developed method, cds from the Arabidopsis thaliana genome were analysed. In total, the algorithm found 9,930 sequences containing one or more potential reading frameshift(s). This is ∼21% of all analysed sequences of the genome. The Type I and Type II error rates were estimated as 11% and 30%, respectively. Similar results were obtained for the genomes of Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Rattus norvegicus and Xenopus tropicalis. Also, the developed algorithm was tested on 17 bacterial genomes. We compared our results with the previously obtained data on the search for potential reading frameshifts in these genomes. This study discussed the possibility that the reading frameshift seems like a relatively frequently encountered mutation; and this mutation could participate in the creation of new genes and proteins.
我们开发了一种新的数学方法，用于检测蛋白质编码序列（cds）中的潜在读框移码。该算法使用动态规划和遗传算法对每个分析序列的三联体周期性进行调整，无需任何预先训练。使用开发的方法，我们分析了拟南芥基因组的 cds。总共，该算法发现了 9930 个序列包含一个或多个潜在的读框移码。这大约是基因组中所有分析序列的 21%。分别估计了 I 型和 II 型错误率为 11%和 30%。对于秀丽隐杆线虫、黑腹果蝇、智人、大鼠和爪蟾的基因组也获得了类似的结果。此外，我们还在 17 个细菌基因组上测试了开发的算法。我们将我们的结果与之前在这些基因组中搜索潜在读框移码获得的数据进行了比较。本研究讨论了读框移码似乎是一种相对常见的突变的可能性，这种突变可能参与新基因和蛋白质的产生。
