Peak Studio: A tool for the visualization and analysis of fragment analysis files

Environmental Microbiology Reports

Volumn 4, Issue 5, 2012, Pages 556-561

  Mccafferty, Jonathan ^a   Reid, Robert ^a   Spencer, Melanie ^a,b   Hamp, Timothy ^a   Fodor, Anthony ^a  

^a University of North Carolina at Charlotte   (United States)

^b LEVINE CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84867178881     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2012.00368.x     Document Type: Article

References (13)

1. Abdo, Z., Schuette, U.M., Bent, S.J., Williams, C.J., Forney, L.J., and Joyce, P. (2006) Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 8 : 929-938.
2. Andrade, L., and Manolakos, E.S. (2003) Signal background estimation and baseline correction algorithms for accurate DNA sequencing. Journal of VLSI 35 : 229-243.
3. Borneman, J., and Triplett, E.W. (1997) Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63 : 2647-2653.
4. Culman, S.W., Bukowski, R., Gauch, H.G., Cadillo-Quiroz, H., and Buckley, D.H. (2009) T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinformatics 10 : 171.
5. Danovaro, R., Luna, G.M., Dell'anno, A., and Pietrangeli, B. (2006) Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl Environ Microbiol 72 : 5982-5989.
6. Fisher, M.M., and Triplett, E.W. (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65 : 4630-4636.
7. Garcia-Martinez, J., Acinas, S.G., Anton, A.I., and Rodriguez-Valera, F. (1999) Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36 : 55-64.
8. Giovannoni, S.J., Britschgi, T.B., Moyer, C.L., and Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345 : 60-63.
9. Ishii, S., Kadota, K., and Senoo, K. (2009) Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data. J Microbiol Methods 78 : 344-350.
10. Liu, W.T., Marsh, T.L., Cheng, H., and Forney, L.J. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63 : 4516-4522.
11. Savitzky, A., and Golay, M.J.E. (1964) Smoothing and differentiation of data by simplified least squares procedures. Anal Chem 36 : 1627-1639.
12. Scallan, U., Liliensiek, A., Clipson, N., and Connolly, J. (2008) ribosort: a program for automated data preparation and exploratory analysis of microbial community fingerprints. Mol Ecol Resour 8 : 95-98.
13. Spencer, M.D., Hamp, T.J., Reid, R.W., Fischer, L.M., Zeisel, S.H., and Fodor, A.A. (2011) Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 140 : 976-986.