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Open Access Research article

Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarray

Víctor Segura1*, Alejandro Toledo-Arana2, Maite Uzqueda1, Iñigo Lasa2 and Arrate Muñoz-Barrutia3

Author Affiliations

1 Genomics, Proteomics and Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain

2 Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología, Universidad Pública de Navarra-Consejo Superior de Investigaciones Científicas-Gobierno de Navarra, Pamplona 31006, Spain

3 Cancer Imaging Laboratory, Center for Applied Medical Research, University of Navarra, Pamplona, Spain

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BMC Bioinformatics 2012, 13:222  doi:10.1186/1471-2105-13-222

Published: 5 September 2012

Additional files

Additional file 1:

R code: Segmentation and visualization functions. Implemented functions in R language to perform PMSW and SCM segmentation and the proposed wavelet-based method for denoising and segmentation. In addition, functions are provided for proper visualization of data, integration of analysis results and evaluation of the obtained transcriptional maps.

Format: R Size: 32KB Download file

Open Data

Additional file 2:

R code: Segmentation analysis of S. cerevisiae. R script for segmentation of the S. cerevisiae dataset and the generation of the figures included in the manuscript.

Format: R Size: 36KB Download file

Open Data

Additional file 3:

R code: Segmentation analysis of S. aureus). R script for the segmentation of the S. aureus dataset and the generation of the figures included in the manuscript.

Format: R Size: 22KB Download file

Open Data

Additional file 4:

Figure S1. Visualization of S. aureus tiling microarray signal along 200 kb of NCTC8325 genome. Each dot corresponds to a probe of the forward strand (top) and reverse strand (bottom) for NCTC8325 wild-type normalized signal. Superimposed pulse signal represents the segmentation obtained using PMSW method. The parameters of the analysis are described in the Results and discussion section of the manuscript.

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Figure S2. Visualization of S. aureus tiling microarray signal along 200 kb of NCTC8325 genome. Each dot corresponds to a probe of the forward strand (top) and reverse strand (bottom) for sigmaB mutant normalized signal. Superimposed pulse signal represents the segmentation obtained using PMSW method. The parameters of the analysis are described in the Results and discussion section of the manuscript.

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Figure S3. Visualization of S. aureus tiling microarray signal along 200 kb of NCTC8325 genome. Each dot corresponds to a probe of the forward strand (top) and reverse strand (bottom) for NCTC8325 wild-type normalized signal. Superimposed pulse signal represents the segmentation obtained using SCM method. The parameters of the analysis are described in the Results and discussion section of the manuscript.

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Figure S4. Visualization of S. aureus tiling microarray signal along 200 kb of NCTC8325 genome. Each dot corresponds to a probe of the forward strand (top) and reverse strand (bottom) for sigmaB mutant normalized signal. Superimposed pulse signal represents the segmentation obtained using SCM method. The parameters of the analysis are described in the Results and discussion section of the manuscript.

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data