Patterns visualized by TraV.

<p>(<b>A</b>) 5′UTR of annotated gene feature. (<b>B</b>) Antisense transcript. (<b>C</b>) Transcriptional activity at a non-annotated region (free transcripts). A, B and C also show strong increases in transcriptional activity, which TraV predicts as transcription start sites. All graphs shown represent data from RNA-Seq experiments performed on <i>B. licheniformis</i> DSM13 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093677#pone.0093677-Wiegand1" target="_blank">[9]</a> (indicated by red boxes). All graphs shown represent data from RNA-Seq experiments performed on <i>B. licheniformis</i> DSM13 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093677#pone.0093677-Wiegand1" target="_blank">[9]</a>.</p

Differential expression.

<p>Differential expression of genes BLi00261 and BLi00262 at selected time points of a fermentative process. Dataset L-I shows the transcriptional activity of <i>B. licheniformis</i> DSM13 at the early exponential growth phase, L-III shows the transcriptional activity at the end of the exponential growth phase and L-V shows the transcriptional activity at the late stationary phase.</p

Strand unspecific mode of TraV.

<p>In case that the available mapped read data does not contain strand specificity information TraV can be switched into the strand unspecific mode in which all mapped reads are summed up to an general activity of a genome locus.</p

Identified UTRs and Free Transcripts in <i>B. licheniformis</i> DSM13.

<p>Identified UTRs and Free Transcripts in <i>B. licheniformis</i> DSM13.</p

Main display of TraV.

<p>Transcriptional activity is depicted by graphs (red graph representing positive strand, blue representing negative strand). Annotated genome information is represented by black arrows. User-provided GFF-based annotations are represented in tracks between the original genome information by coloured arrows (green arrow in this figure).</p

Oligonucleotides used in this study.

<p>*Restriction sites within the oligonucleotide sequences are printed in bold.</p><p>Oligonucleotides used in this study.</p

Growth behavior of <i>B</i>. <i>licheniformis</i> DSM13 and its derivatives after induction with mitomycin C.

<p>The KLETT Units represent the turbidity of the culture. The vertical red line at 2 hours marks the time point of induction with 0.5 μg/ml mitomycin C. Induced cultures (MC) are marked with filled symbols and non-induced cultures with open symbols. <i>B</i>. <i>licheniformis</i> DSM13 shows a loss in turbidity 3 hours after induction with mitomycin C and <i>B</i>. <i>licheniformis</i> ΔPBSX after 6 hours. The strain <i>B</i>. <i>licheniformis</i> ΔPBSX-ΔBLi_Pp3 exhibited no decrease of turbidity after mitomycin C treatment.</p

<i>Bacillus</i> strains used in this study.

<p><i>Bacillus</i> strains used in this study.</p

Prophage regions of <i>B</i>. <i>licheniformis</i> DSM13.

<p>*The average host genome GC content is 46.2. The size of the prophage regions refers to the sequence between the insertion repeats. For BLi_Pp2 the range from the first to the last identified phage gene was used since no insertion repeats were found.</p><p>^# Size of the insertion repeats with the number of variations in bp.</p><p>Prophage regions of <i>B</i>. <i>licheniformis</i> DSM13.</p

Phage activity graphs on the genome of <i>B</i>. <i>licheniformis</i> DSM13.

<p><i>B</i>. <i>licheniformis</i> phage DNA was sequenced by next generation sequencing (NGS) and sequences were mapped on the genome of <i>B</i>. <i>licheniformis</i> DSM13. The results are displayed in NPKM values calculated by TraV [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120759#pone.0120759.ref026" target="_blank">26</a>]. Prophage regions BLi_Pp1 – BLi_Pp7 are marked with grey bars. A: The phage DNA read mapping of <i>B</i>. <i>licheniformis</i> DSM13 shows a even distribution of reads over the whole genome as well as read accumulations around the origin of replication and also in some further regions, especially in BLi_Pp3. B: The <i>B</i>. <i>licheniformis</i> ΔPBSX phage DNA read mapping (green graph) shows a strong read accumulation in the region BLi_Pp3 compared to the <i>B</i>. <i>licheniformis</i> DSM13 read mapping (red graph), and a slight read accumulation in region BLi_Pp6. The <i>B</i>. <i>licheniformis</i> ΔPBSX-ΔBLi_Pp3 phage DNA read mapping (blue graph, result of the first experiment is shown) exhibits a distinct read accumulation in BLi_Pp6.</p