Journal
BMC BIOINFORMATICS
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12859-015-0793-8
Keywords
Feature subset selection; Comparative metagenomics; Open-source software
Categories
Funding
- NSF [1120622]
- DoE [SC004335]
- Drexel's University Research Computing Facility
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [1120622] Funding Source: National Science Foundation
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Background: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using alpha- & beta-diversity. Feature subset selection -a sub-field of machine learning -can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. Results: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. Conclusions: We have made the software implementation of Fizzy available to the public under the GNU GPL license.
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