A systematic and extensible approach to DNA primer design for whole gene synthesis
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.
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| Other Authors: | |
| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2007
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| Online Access: | http://hdl.handle.net/1721.1/37059 |
| _version_ | 1811087701669052416 |
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| author | Wozniak, Amanda Victrix Allen |
| author2 | Thomas F. Knight, Jr. |
| author_facet | Thomas F. Knight, Jr. Wozniak, Amanda Victrix Allen |
| author_sort | Wozniak, Amanda Victrix Allen |
| collection | MIT |
| description | Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005. |
| first_indexed | 2024-09-23T13:50:39Z |
| format | Thesis |
| id | mit-1721.1/37059 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T13:50:39Z |
| publishDate | 2007 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/370592019-04-10T09:05:33Z A systematic and extensible approach to DNA primer design for whole gene synthesis Wozniak, Amanda Victrix Allen Thomas F. Knight, Jr. 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, 2005. Includes bibliographical references (leaves 93-96). The future of synthetic biology research hinges upon the development of accurate and inexpensive whole gene synthesis technologies. Recent advances in the purification of solid-phase manufactured oligonucleotides make it possible to manufacture whole genes by polymerase chain reaction methods. Yet, despite the improvement in laboratory methods, whole gene synthesis is not rapidly progressing because most gene design software takes an excessively naive approach to the complex problem of designing component oligonucleotides for whole gene synthesis. The synthetic biology community needs a flexible, robust and optimal primer design tool. We present the software design for a tool which designs oligonucleotides that are compatible with a wide variety of oligo purification and whole gene assembly protocols. Our design strategy uses physical sequence feature identification, optimal artificial intelligence search techniques, and sequence optimisation via intelligent codon substitution to produce near-optimal oligonucleotide arrays. We address all aspects of the oligonucleotide design problem, from physical constraints to the computational overhead involved in searching for an optimal solution, and provide an extensive set of data structures and algorithms. by Amanda Victrix Allen Wozniak. M.Eng. 2007-04-03T17:07:20Z 2007-04-03T17:07:20Z 2005 2005 Thesis http://hdl.handle.net/1721.1/37059 82462280 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 96 leaves application/pdf Massachusetts Institute of Technology |
| spellingShingle | Electrical Engineering and Computer Science. Wozniak, Amanda Victrix Allen A systematic and extensible approach to DNA primer design for whole gene synthesis |
| title | A systematic and extensible approach to DNA primer design for whole gene synthesis |
| title_full | A systematic and extensible approach to DNA primer design for whole gene synthesis |
| title_fullStr | A systematic and extensible approach to DNA primer design for whole gene synthesis |
| title_full_unstemmed | A systematic and extensible approach to DNA primer design for whole gene synthesis |
| title_short | A systematic and extensible approach to DNA primer design for whole gene synthesis |
| title_sort | systematic and extensible approach to dna primer design for whole gene synthesis |
| topic | Electrical Engineering and Computer Science. |
| url | http://hdl.handle.net/1721.1/37059 |
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