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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.
This article was published in the following journal.
Name: DNA research : an international journal for rapid publication of reports on genes and genomes
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Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
A plant homeotic protein involved in the development of stamens and carpels of Arabidopsis thaliana. It is a DNA-binding protein that contains the MADS-box domain. It is one of the four founder proteins that structurally define the superfamily of MADS DOMAIN PROTEINS.
The systematic search and discovery of natural substances which may have potential commercial applications.
One of four major classes of mammalian serine/threonine specific protein phosphatases. Protein phosphatase 2C is a monomeric enzyme about 42 kDa in size. It shows broad substrate specificity dependent on divalent cations (mainly manganese and magnesium). Three isozymes are known in mammals: PP2C -alpha, -beta and -gamma. In yeast, there are four PP2C homologues: phosphatase PTC1 that have weak tyrosine phosphatase activity, phosphatase PTC2, phosphatase PTC3, and PTC4. Isozymes of PP2C also occur in Arabidopsis thaliana where the kinase-associated protein phosphatase (KAPP) containing a C-terminal PP2C domain, dephosphorylates Ser/Thr receptor-like kinase RLK5.
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