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BIOINFORMATICS
2012

SSuMMo: rapid analysis, comparison and visualization of microbial communities

11 years 6 months ago
SSuMMo: rapid analysis, comparison and visualization of microbial communities
Motivation: Next-generation sequencing methods are generating increasingly massive datasets, yet still do not fully capture genetic diversity in the richest environments. To understand such complicated and elusive systems, effective tools are needed to assist with delineating the differences found in and between community datasets. Results: The Small Subunit Markov Modeler (SSuMMo) was developed to probabilistically assign SSU rRNA gene fragments from any sequence dataset to recognized taxonomic clades, producing consistent, comparable cladograms. Accuracy tests predicted >90% of genera correctly for sequences downloaded from public reference databases. Sequences from a next-generation sequence dataset, sampled from lean, overweight and obese individuals, were analysed to demonstrate parallel visualization of comparable datasets. SSuMMo shows potential as a valuable curatorial tool, as numerous incorrect and outdated taxonomic entries and annotations were identified in public data...
Alex L. B. Leach, James P. J. Chong, Kelly R. Rede
Added 29 Sep 2012
Updated 29 Sep 2012
Type Journal
Year 2012
Where BIOINFORMATICS
Authors Alex L. B. Leach, James P. J. Chong, Kelly R. Redeker
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