A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation
Within the realms of human thoughts on nature, Fourier analysis is considered as one of the greatest ideas currently put forwarded. The Fourier transform shows that any periodic function can be rewritten as the sum of sinusoidal functions. Having a Fourier transform view on real-world problems like...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997877/?tool=EBI |
| _version_ | 1811154303919849472 |
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| author | Roxana Abadeh Mehdi Aminafshar Mostafa Ghaderi-Zefrehei Mohammad Chamani |
| author_facet | Roxana Abadeh Mehdi Aminafshar Mostafa Ghaderi-Zefrehei Mohammad Chamani |
| author_sort | Roxana Abadeh |
| collection | DOAJ |
| description | Within the realms of human thoughts on nature, Fourier analysis is considered as one of the greatest ideas currently put forwarded. The Fourier transform shows that any periodic function can be rewritten as the sum of sinusoidal functions. Having a Fourier transform view on real-world problems like the DNA sequence of genes, would make things intuitively simple to understand in comparison with their initial formal domain view. In this study we used discrete Fourier transform (DFT) on DNA sequences of a set of genes in the bovine genome known to govern milk production, in order to develop a new gene clustering algorithm. The implementation of this algorithm is very user-friendly and requires only simple routine mathematical operations. By transforming the configuration of gene sequences into frequency domain, we sought to elucidate important features and reveal hidden gene properties. This is biologically appealing since no information is lost via this transformation and we are therefore not reducing the number of degrees of freedom. The results from different clustering methods were integrated using evidence accumulation algorithms to provide in insilico validation of our results. We propose using candidate gene sequences accompanied by other genes of biologically unknown function. These will then be assigned some degree of relevant annotation by using our proposed algorithm. Current knowledge in biological gene clustering investigation is also lacking, and so DFT-based methods will help shine a light on use of these algorithms for biological insight. |
| first_indexed | 2024-04-10T04:13:29Z |
| format | Article |
| id | doaj.art-1b012864d0fb4a6486692cdfe0912909 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-10T04:13:29Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-1b012864d0fb4a6486692cdfe09129092023-03-12T05:32:30ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01183A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformationRoxana AbadehMehdi AminafsharMostafa Ghaderi-ZefreheiMohammad ChamaniWithin the realms of human thoughts on nature, Fourier analysis is considered as one of the greatest ideas currently put forwarded. The Fourier transform shows that any periodic function can be rewritten as the sum of sinusoidal functions. Having a Fourier transform view on real-world problems like the DNA sequence of genes, would make things intuitively simple to understand in comparison with their initial formal domain view. In this study we used discrete Fourier transform (DFT) on DNA sequences of a set of genes in the bovine genome known to govern milk production, in order to develop a new gene clustering algorithm. The implementation of this algorithm is very user-friendly and requires only simple routine mathematical operations. By transforming the configuration of gene sequences into frequency domain, we sought to elucidate important features and reveal hidden gene properties. This is biologically appealing since no information is lost via this transformation and we are therefore not reducing the number of degrees of freedom. The results from different clustering methods were integrated using evidence accumulation algorithms to provide in insilico validation of our results. We propose using candidate gene sequences accompanied by other genes of biologically unknown function. These will then be assigned some degree of relevant annotation by using our proposed algorithm. Current knowledge in biological gene clustering investigation is also lacking, and so DFT-based methods will help shine a light on use of these algorithms for biological insight.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997877/?tool=EBI |
| spellingShingle | Roxana Abadeh Mehdi Aminafshar Mostafa Ghaderi-Zefrehei Mohammad Chamani A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation PLoS ONE |
| title | A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation |
| title_full | A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation |
| title_fullStr | A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation |
| title_full_unstemmed | A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation |
| title_short | A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation |
| title_sort | new gene tree algorithm employing dna sequences of bovine genome using discrete fourier transformation |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997877/?tool=EBI |
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