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Bonnie Berger. Yu, Michael Ku Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science 2011-11-01T19:48:26Z 2011-11-01T19:48:26Z 2011 2011 http://hdl.handle.net/1721.1/66817 757176132 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. 65 p. eng Massachusetts Institute of Technology 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 Electrical Engineering and Computer Science. 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 Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="d4495ca2-9353-46a3-b627-b9bc99417205"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Structure-based realignment of non-coding RNAs in multiple whole genome alignments</Title> <Subtitle>Alignment and prediction on non-coding RNAs</Subtitle> <Subtitle>Structure-based realignment of non-coding ribonucleic acids in multiple whole genome alignments</Subtitle> <Subtitle>Alignment and prediction on non-coding ribonucleic acids</Subtitle> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2011</PublicationDate> <Authors> <Author> <DisplayName>Yu, Michael Ku</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Electrical Engineering and Computer Science.</Keyword> <Abstract>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.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>