Structure-based realignment of non-coding RNAs in multiple whole genome alignments
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2011
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| Online Access: | http://hdl.handle.net/1721.1/66817 |
| _version_ | 1811093157969920000 |
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| author | Yu, Michael Ku |
| author2 | Bonnie Berger. |
| author_facet | Bonnie Berger. Yu, Michael Ku |
| author_sort | Yu, Michael Ku |
| collection | MIT |
| description | Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011. |
| first_indexed | 2024-09-23T15:40:35Z |
| format | Thesis |
| id | mit-1721.1/66817 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T15:40:35Z |
| publishDate | 2011 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/668172019-04-12T14:58:28Z Structure-based realignment of non-coding RNAs in multiple whole genome alignments Alignment and prediction on non-coding RNAs Structure-based realignment of non-coding ribonucleic acids in multiple whole genome alignments Alignment and prediction on non-coding ribonucleic acids Yu, Michael Ku Bonnie Berger. Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science. Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science. Electrical Engineering and Computer Science. Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011. Cataloged from PDF version of thesis. Includes bibliographical references (p. 62-65). Whole genome alignments have become a central tool in biological sequence analysis. A major application is the de novo prediction of non-coding RNAs (ncRNAs) from structural conservation visible in the alignment. However, current methods for constructing genome alignments do so by explicitly optimizing for sequence similarity but not structural similarity. Therefore, de novo prediction of ncRNAs with high structural but low sequence conservation is intrinsically challenging in a genome alignment because the conservation signal is typically hidden. This study addresses this problem with a method for genome-wide realignment of potential ncRNAs according to structural similarity. Doing so reveals thousands of new high-confidence ncRNA predictions with particularly low sequence conservation from an alignment of 12 Drosophila genomes and hundreds from an alignment of 28 vertebrate genomes in the Encode project. by Michael Ku Yu. M.Eng. 2011-11-01T19:48:26Z 2011-11-01T19:48:26Z 2011 2011 Thesis http://hdl.handle.net/1721.1/66817 757176132 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 65 p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Electrical Engineering and Computer Science. Yu, Michael Ku Structure-based realignment of non-coding RNAs in multiple whole genome alignments |
| title | Structure-based realignment of non-coding RNAs in multiple whole genome alignments |
| title_full | Structure-based realignment of non-coding RNAs in multiple whole genome alignments |
| title_fullStr | Structure-based realignment of non-coding RNAs in multiple whole genome alignments |
| title_full_unstemmed | Structure-based realignment of non-coding RNAs in multiple whole genome alignments |
| title_short | Structure-based realignment of non-coding RNAs in multiple whole genome alignments |
| title_sort | structure based realignment of non coding rnas in multiple whole genome alignments |
| topic | Electrical Engineering and Computer Science. |
| url | http://hdl.handle.net/1721.1/66817 |
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