Genome2D: visualization tool for rapid analysis of bacterial transcriptome data.
Richard J.S. Baerends, Wiep Klaas Smits, Anne de Jong #, Leendert W. Hamoen, Jan Kok and Oscar P. Kuipers.
# corresponding author
Genome Biology, 5, 5, R37.
Abstract
Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and other customized data sets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the analysis of transcriptome data by using different colour ranges to depict differences in gene expression levels on a genome map. Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge on expression level cut-off values.
The programme includes algorithms to extract such information. Images and data tables from Genome2D can easily be exported for further use in other presentation programs. Features of Genome2D are illustrated by the prediction of the CcpA-regulon in Lactococcus lactis IL1403 and the analysis of the ComK-regulon in Bacillus subtilis 8G5.
Online help is available here.
How to obtain Genome2D ? (Click here).
file1_cre-boxes.doc |
List of cre-box sequences found in Gram-positive bacteria |
file2_cre-box_weightmatrix.doc |
Screendump of Genome2D showing the cre-box weight matrix |
file3_il1403-elements-color.txt |
Genome2D input file with the coordinates of the identified cre-boxes and promoter elements in the genome of L. lactis IL1403 (colour file). |
file4_Table2.doc |
Table of identified cre-boxes in promoters of genes in the L. lactis genome. |
Genome data (NCBI) | L. lactis strain IL1403 GenBank file B. subtilis strain 168 GenBank file |
List cre-box sequences for trained set search | cre-boxes.txt [Genome2D_ready_file]
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Prediction cre-boxes in L. lactis IL1403 (cut-off 8) | il1403-crebox.xls il1403-crebox.txt |
Location of predicted | minus35.txt minus10.txt |
Overview Genome2D features | Table 1.pdf |