Home About us MoEF Contact us Sitemap Tamil Website  
About Envis
Whats New
Microorganisms
Research on Microbes
Database
Bibliography
Publications
Library
E-Resources
Microbiology Experts
Events
Online Submission
Access Statistics

Site Visitors

blog tracking


 
Bioinformatics
Vol.28, No.5, 2012; Pages: 679 - 86

SSuMMo: rapid analysis, comparison and visualization of microbial communities

Leach AL, Chong JP, Redeker KR

Department of Biology, University of York, York YO10 5DD, UK.

Abstract

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 SSuMMo shows potential as a valuable curatorial tool, as numerous incorrect and outdated taxonomic entries and annotations were identified in public databases. Availability and implementation: SSuMMo is GPLv3 open source Python software, available at http://code.google.com/p/ssummo/. Taxonomy and HMM databases can be downloaded from http://bioltfws1.york.ac.uk/ssummo/.

SUPPLEMENTARY INFORMATION:

Supplemental materials are available at Bioinformatics Online.

 

Keywords:


 

 
Copyright © 2005 ENVIS Centre ! All rights reserved
This site is optimized for 1024 x 768 screen resolution