SeqWord Genome Browser: A Tool for Analyzing Bacterial Genomes
Author Information
Author(s): Ganesan Hamilton, Rakitianskaia Anna S, Davenport Colin F, Tümmler Burkhard, Reva Oleg N
Primary Institution: University of Pretoria
Hypothesis
The research aims to develop a web-based tool for oligonucleotide usage statistical analysis in functional genomics.
Conclusion
The SeqWord Genome Browser provides comprehensive statistical parameters for analyzing bacterial genomes and identifying atypical genomic regions.
Supporting Evidence
- The SWGB applet visualizes DNA compositional variations in bacterial genomes.
- It allows for the identification of horizontally transferred genomic islands.
- The applet has been tested on 1243 sequences of different microorganisms.
Takeaway
The SeqWord Genome Browser is a tool that helps scientists look at DNA sequences to find unusual parts of bacteria's genetic code.
Methodology
The tool uses oligonucleotide usage patterns to visualize and identify divergent genomic regions in bacterial genomes.
Potential Biases
The method may be influenced by the presence of homogenous DNA insertions, affecting the core genome's definition.
Limitations
The analysis may miss some genomic islands due to the sliding window size and the nature of the genomic signatures.
Digital Object Identifier (DOI)
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