Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.
dynamic programming
genetic algorithm
periodicity
reading frameshift
Journal
DNA research : an international journal for rapid publication of reports on genes and genomes
ISSN: 1756-1663
Titre abrégé: DNA Res
Pays: England
ID NLM: 9423827
Informations de publication
Date de publication:
01 Apr 2019
01 Apr 2019
Historique:
received:
27
04
2018
accepted:
07
12
2018
pubmed:
7
2
2019
medline:
6
8
2019
entrez:
7
2
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 30726896
pii: 5306610
doi: 10.1093/dnares/dsy046
pmc: PMC6476729
doi:
Types de publication
Journal Article
Langues
eng
Pagination
157-170Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
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