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Using emergent self-organizing maps to identify marine group II archaea genomic fragments from uncharacterized microbial metagenomic sequences

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dc.contributor.advisor Edward F. DeLong. en_US
dc.contributor.author Hillmer, Rachel A en_US
dc.contributor.other Massachusetts Institute of Technology. Dept. of Biological Engineering. en_US
dc.date.accessioned 2011-05-23T17:57:44Z
dc.date.available 2011-05-23T17:57:44Z
dc.date.copyright 2010 en_US
dc.date.issued 2010 en_US
dc.identifier.uri http://hdl.handle.net/1721.1/62987
dc.description Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2010. en_US
dc.description Cataloged from PDF version of thesis. en_US
dc.description Includes bibliographical references. en_US
dc.description.abstract The validity and usefulness of clustering marine group II tetranucleotide signatures using emergent self-organizing maps was investigated. Fosmids from the HF200 library were chosen for sequencing based on end-sequence tetranucleotide clustering with group II seed sequences, as well as blastx homology. Fosmids were sequenced using a single 454- titanium sequencing run, and contigs subsequently assembled in silico. A total of 99 contigs over 20kb were retrieved, at least 72 of which belong to the marine group II archaea. The phylogenetic substructure of the marine group II archaeal clusters having more than a few representatives was investigated, by clustering tetranucleotide signatures of group II contigs over 20kb, also with an emergent self-organizing map. The distribution of these clusters in the Hawaii Ocean Time Series depth profile fosmid libraries in the DeLong lab were mapped onto depth profiles from three independent cruises. en_US
dc.description.statementofresponsibility by Rachel A. Hillmer. en_US
dc.format.extent 117p. en_US
dc.language.iso eng en_US
dc.publisher Massachusetts Institute of Technology en_US
dc.rights 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. en_US
dc.rights.uri http://dspace.mit.edu/handle/1721.1/7582 en_US
dc.subject Biological Engineering. en_US
dc.title Using emergent self-organizing maps to identify marine group II archaea genomic fragments from uncharacterized microbial metagenomic sequences en_US
dc.type Thesis en_US
dc.description.degree S.M. en_US
dc.contributor.department Massachusetts Institute of Technology. Dept. of Biological Engineering. en_US
dc.identifier.oclc 720389685 en_US


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