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

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biological Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2010

Author dc:creator

• Hillmer, Rachel A

Advisor dc:contributor.advisor

• Edward F. DeLong.

• Biological Engineering.

Statement dc:rights

• MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/62987

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/62987