Using emergent self-organizing maps to identify marine group II archaea genomic fragments from uncharacterized microbial metagenomic sequences
Name
720389685-MIT.pdf
Description
Full printable version
Size
17.44 MB
Format
Adobe PDF
Checksum (MD5)
bcf21ea53e68ff4654a55caf0f82ea10
Author(s)
Hillmer, Rachel A
Advisor(s)
Edward F. DeLong.
Date Issued
2010
Publisher
Massachusetts Institute of Technology
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.
Description
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2010.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Subjects
Biological Engineering.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
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MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided.
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