Two algorithmic problems in analyzing genetic and epigenetic variations
Single nucleotide polymorphism (SNP) is the most common type of genetic variations.Accurate detection of SNPs is crucial to many downstream studies. To detect SNPs, MALDI-TOF mass spectrometry combined with base-specific cleavage reactions has been employed in many experiments. A new SNP detecting al...
| Egile nagusia: | |
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| Beste egile batzuk: | |
| Formatua: | Thesis |
| Hizkuntza: | English |
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2015
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| Gaiak: | |
| Sarrera elektronikoa: | https://hdl.handle.net/10356/65312 |
| _version_ | 1826120504205901824 |
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| author | Sun, Ruimin |
| author2 | Chen Xin |
| author_facet | Chen Xin Sun, Ruimin |
| author_sort | Sun, Ruimin |
| collection | NTU |
| description | Single nucleotide polymorphism (SNP) is the most common type of genetic variations.Accurate detection of SNPs is crucial to many downstream studies. To detect SNPs, MALDI-TOF mass spectrometry combined with base-specific cleavage reactions has been employed in many experiments. A new SNP detecting algorithm is presented in the thesis, together with the performance evaluation of its implemented program called SnpMs.Results demonstrate that SnpMs has a high ability to detect SNP mutations accurately. Cytosine methylation plays an important role in many biological regulation processes. The current golden standard method for analyzing cytosine methylation is BS-Seq. In this thesis, a new tool called TAMeBS is introduced to align BS-Seq reads and estimate the methylation status of each cytosine. Experimental results on both simulated and real data showed that TAMeBS could detect many more uniquely best mapped reads while achieving a good balance between sensitivity and precision. |
| first_indexed | 2024-10-01T05:17:31Z |
| format | Thesis |
| id | ntu-10356/65312 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:17:31Z |
| publishDate | 2015 |
| record_format | dspace |
| spelling | ntu-10356/653122023-02-28T23:45:04Z Two algorithmic problems in analyzing genetic and epigenetic variations Sun, Ruimin Chen Xin School of Physical and Mathematical Sciences DRNTU::Science::Mathematics::Discrete mathematics::Algorithms DRNTU::Science::Biological sciences::Genetics Single nucleotide polymorphism (SNP) is the most common type of genetic variations.Accurate detection of SNPs is crucial to many downstream studies. To detect SNPs, MALDI-TOF mass spectrometry combined with base-specific cleavage reactions has been employed in many experiments. A new SNP detecting algorithm is presented in the thesis, together with the performance evaluation of its implemented program called SnpMs.Results demonstrate that SnpMs has a high ability to detect SNP mutations accurately. Cytosine methylation plays an important role in many biological regulation processes. The current golden standard method for analyzing cytosine methylation is BS-Seq. In this thesis, a new tool called TAMeBS is introduced to align BS-Seq reads and estimate the methylation status of each cytosine. Experimental results on both simulated and real data showed that TAMeBS could detect many more uniquely best mapped reads while achieving a good balance between sensitivity and precision. DOCTOR OF PHILOSOPHY (SPMS) 2015-07-16T04:18:14Z 2015-07-16T04:18:14Z 2015 2015 Thesis Sun, R. (2015). Two algorithmic problems in analyzing genetic and epigenetic variations. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/65312 10.32657/10356/65312 en 134 p. application/pdf |
| spellingShingle | DRNTU::Science::Mathematics::Discrete mathematics::Algorithms DRNTU::Science::Biological sciences::Genetics Sun, Ruimin Two algorithmic problems in analyzing genetic and epigenetic variations |
| title | Two algorithmic problems in analyzing genetic and epigenetic variations |
| title_full | Two algorithmic problems in analyzing genetic and epigenetic variations |
| title_fullStr | Two algorithmic problems in analyzing genetic and epigenetic variations |
| title_full_unstemmed | Two algorithmic problems in analyzing genetic and epigenetic variations |
| title_short | Two algorithmic problems in analyzing genetic and epigenetic variations |
| title_sort | two algorithmic problems in analyzing genetic and epigenetic variations |
| topic | DRNTU::Science::Mathematics::Discrete mathematics::Algorithms DRNTU::Science::Biological sciences::Genetics |
| url | https://hdl.handle.net/10356/65312 |
| work_keys_str_mv | AT sunruimin twoalgorithmicproblemsinanalyzinggeneticandepigeneticvariations |