PhaMers Identifies Novel Bacteriophage Sequences from Thermophilic Hot Springs
Abstract/Contents
- Abstract
- Discovering novel phage sequences from metagenomic data is often challenging. This study presents PhaMers (Phage k-Mers), a phage identification tool that uses supervised learning to identify metagenomic sequences (contigs) as phage or non-phage on the basis of tetranucleotide frequencies. PhaMers compares the tetranucleotide frequencies of metagenomic contigs to those of phage and bacteria reference genomes from online databases. Using PhaMers, we identified 103 novel phage sequences in hot spring samples from Yellowstone National Park. We applied a microfluidic-based mini-metagenomic approach to sequence environmental samples and produce metagenomic sequence datasets. We analyzed assembled contigs using PhaMers and VirSorter, a publicly available phage identification and annotation pipeline. We present the performance of PhaMers in identifying genomic fragments of phages and its ability to predict phage taxonomic classification. We also present putative hosts and taxa for some novel phage sequences. PhaMers is available for public use at https://github.com/jondeaton/PhaMers.
Description
| Type of resource | text |
|---|---|
| Date created | [ca. October 2015 - February 2017] |
Creators/Contributors
| Author | Deaton, Jonathan |
|---|---|
| Primary advisor | Yu, Brian |
| Principal investigator | Quake, Stephen |
| Advisor | Altman, Russ |
| Degree granting institution | Stanford University, Department of Bioengineering |
Subjects
| Subject | Bacteriophage |
|---|---|
| Subject | Phage |
| Subject | Metagenomics |
| Subject | Yellowstone |
| Subject | PhaMers |
| Genre | Thesis |
Bibliographic information
| Related item |
|
|---|---|
| Location | https://purl.stanford.edu/ts843mx8043 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
Preferred citation
- Preferred Citation
- Deaton, Jonathan; Yu, Brian; Quake, Stephen; and Altman, Russ. PhaMers Identifies Novel Bacteriophage Sequences from Thermophilic Hot Springs. Stanford Digital Repository. Available at: http://purl.stanford.edu/ts843mx8043
Collection
Undergraduate Theses, School of Engineering
View other items in this collection in SearchWorksContact information
- Contact
- jdeaton@stanford.edu
Also listed in
Loading usage metrics...