Integrating genomic conservation data with motif discovery
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.
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| Format: | Thesis |
| Language: | en_US |
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Massachusetts Institute of Technology
2005
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| Online Access: | http://hdl.handle.net/1721.1/28493 |
| _version_ | 1826193656059527168 |
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| author | Danford, Timothy W. (Timothy William), 1979- |
| author2 | David K. Gifford. |
| author_facet | David K. Gifford. Danford, Timothy W. (Timothy William), 1979- |
| author_sort | Danford, Timothy W. (Timothy William), 1979- |
| collection | MIT |
| description | Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004. |
| first_indexed | 2024-09-23T09:42:37Z |
| format | Thesis |
| id | mit-1721.1/28493 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:42:37Z |
| publishDate | 2005 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/284932019-04-10T23:03:41Z Integrating genomic conservation data with motif discovery Danford, Timothy W. (Timothy William), 1979- David K. Gifford. 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 (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004. Includes bibliographical references (leaves 94-99). We formalize a probabilistic model of inter-species sequence conservation for motif discovery, and demonstrate that adding large-scale genomic conservation data to an existing motif discovery procedure improves the quality of that procedure's results. Existing motif discovery algorithms reveal binding motifs that are statistically over-represented in small sets of promoter regions. To the extent that binding motifs form a reliable part of a cell's regulatory apparatus, and that apparatus is preserved across closely related species, these binding motifs should also be conserved in the corresponding genomes. Previous studies have tried to assess levels of conservation in genomic fragments of several yeast species. Our approach computes the conditional probability of inter-species sequences, and uses this probability measure to maximize the likelihood of the data from different species with a motif model. by Timothy W. Danford. S.M. 2005-09-26T20:45:03Z 2005-09-26T20:45:03Z 2004 2004 Thesis http://hdl.handle.net/1721.1/28493 57303928 en_US 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 99 leaves 4648981 bytes 4660362 bytes application/pdf application/pdf application/pdf Massachusetts Institute of Technology |
| spellingShingle | Electrical Engineering and Computer Science. Danford, Timothy W. (Timothy William), 1979- Integrating genomic conservation data with motif discovery |
| title | Integrating genomic conservation data with motif discovery |
| title_full | Integrating genomic conservation data with motif discovery |
| title_fullStr | Integrating genomic conservation data with motif discovery |
| title_full_unstemmed | Integrating genomic conservation data with motif discovery |
| title_short | Integrating genomic conservation data with motif discovery |
| title_sort | integrating genomic conservation data with motif discovery |
| topic | Electrical Engineering and Computer Science. |
| url | http://hdl.handle.net/1721.1/28493 |
| work_keys_str_mv | AT danfordtimothywtimothywilliam1979 integratinggenomicconservationdatawithmotifdiscovery |