Expanding De Novo Repeat Search to Multiple Spaced Seeds
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Miami University / OhioLINK
2018
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| Online Access: | http://rave.ohiolink.edu/etdc/view?acc_num=miami1527860222418868 |
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ndltd-OhioLink-oai-etd.ohiolink.edu-miami15278602224188682021-08-03T07:07:09Z Expanding De Novo Repeat Search to Multiple Spaced Seeds Skon, Luke C. Computer Science Bioinformatics In the field of Bioinformatics, there have been many tools created to detect repetitive elements in DNA. Transposable Elements, segments of DNA that can be copied across the genome, make up the majority of this repetition. Identifying these Transposable Elements is a necessary step in order to investigate them in their own right and also to permit us to omit them from the genome to narrow the search space of that genome. De novo Transposable Element identification tools can identify these elements without any libraries or prior information about the genome. The RAIDER algorithm (Schaeffer 2016) was developed previously to improve upon the performance of other search tools. This algorithm was enhanced in the tool phRAIDER by including elements from a homology tool known as Pattern-Hunter. Pattern-Hunter uses one or more spaced seeds, which allows for fast and inexact matches between strings. The most recent iteration of phRAIDER only allows for one spaced seed to be used. The purpose of this study is to identify whether the use of multiple spaced seeds can improve sensitivity and specificity when scanning for Transposable Elements. 2018-06-22 English text Miami University / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=miami1527860222418868 http://rave.ohiolink.edu/etdc/view?acc_num=miami1527860222418868 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws. |
| collection |
NDLTD |
| language |
English |
| sources |
NDLTD |
| topic |
Computer Science Bioinformatics |
| spellingShingle |
Computer Science Bioinformatics Skon, Luke C. Expanding De Novo Repeat Search to Multiple Spaced Seeds |
| author |
Skon, Luke C. |
| author_facet |
Skon, Luke C. |
| author_sort |
Skon, Luke C. |
| title |
Expanding De Novo Repeat Search to Multiple Spaced Seeds |
| title_short |
Expanding De Novo Repeat Search to Multiple Spaced Seeds |
| title_full |
Expanding De Novo Repeat Search to Multiple Spaced Seeds |
| title_fullStr |
Expanding De Novo Repeat Search to Multiple Spaced Seeds |
| title_full_unstemmed |
Expanding De Novo Repeat Search to Multiple Spaced Seeds |
| title_sort |
expanding de novo repeat search to multiple spaced seeds |
| publisher |
Miami University / OhioLINK |
| publishDate |
2018 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=miami1527860222418868 |
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AT skonlukec expandingdenovorepeatsearchtomultiplespacedseeds |
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