Suvorova YM et al. (2019), Search for potential reading frameshifts in cds...

XB-ART-55686

DNA Res 2019 Apr 01;262:157-170. doi: 10.1093/dnares/dsy046.

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Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.

Suvorova YM , Korotkova MA , Skryabin KG , Korotkov EV .

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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.

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References [+] :

Antonov, GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. 2013, Pubmed

	Figure 1. (A) The TP matrix is shown for the sequence S={atc}50. (B) The phase TP in a fragment of the sequence S. A base g is inserted in the middle of the sequence. The phase Fa = 0 was before the insertion of g, because there is an agreement between the columns of the matrix and the positions of the codons as 1 => 1, 2 => 2, 3 => 3, respectively. Fa = 1 after the insertion of g, because the following agreement is observed: 1 => 2, 2 => 3, 3 => 1. (C) The TP matrix for the sequence S={atcgga}25.
	Figure 2. A block diagram of the algorithm for the optimization of random matrices M(3,16) from the MR set, used to search a matrix with the largest mFmax.
	Figure 3. The idea of the algorithm is to create a random matrix Wr, (or a set of random matrices), then optimize it with a genetic algorithm and get the W1 matrix as a result of optimization.
	Figure 4. The dependence of the d value (see Equation 2) on the TP, of the analysed sequence. The TP was calculated using the TP matrix33 and is expressed in the arguments of the normal distribution and is shown along the x-axis.
	Figure 5. Scheme of division of mFmax on V1, V2 and V3 (see Section 2.4).
	Figure 6. Distribution of shifts position in the sequence of a gene. The x-axis shows the distance as a percentage of the beginning of the gene (with step equals to 5%), the y-axis shows the percentage of shifts per interval of 5%. The black bars—the data from the work,21 the white—the data of our work. The leftmost and rightmost bars show the number of frameshifts found outside the cds from the work.21
	Figure 7. Distribution of the distance between paired compensating shifts of the TP phase in the Arabidopsis thaliana genome.