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Strainer: software for analysis of population variation in community genomic datasets
John M Eppley1, Gene W Tyson, Wayne M Getz
1Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA. jmeppley@gmail.com
BMC Bioinformatics
|October 19, 2007
Summary
This study introduces Strainer, a bioinformatics tool for analyzing genetic variation in microbial communities. Strainer visualizes sequence variation and reconstructs strain variants, aiding evolutionary and ecological studies.
Area of Science:
- Microbial genomics
- Bioinformatics
- Population genetics
Background:
- Metagenomic analyses reveal genetic variation in natural microbial populations.
- Bioinformatic tools are needed for analyzing this variation and inferring evolutionary processes.
Purpose of the Study:
- To develop a software package for analyzing and visualizing genetic variation in populations.
- To reconstruct strain variants from metagenomic data.
Main Methods:
- Developed the Strainer software package.
- Clustered sequencing reads based on single nucleotide polymorphism patterns.
- Generated predicted gene and protein variant sequences.
Main Results:
- The software enables analysis and visualization of genetic variation.
- Identified conserved intergenic regulatory sequences.
- Quantified recombination events within populations.
Conclusions:
- Strainer facilitates analysis of heterogeneity in natural microbial communities.
- The tool aids in generating gene and protein sequences for functional, ecological, and evolutionary analyses.
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