Merging multiple sets of loci.

<p>SeaSight offers several methods to combine locus data from different sources. Strong horizontal lines represent genomic loci, fine lines represent reads in the top panel. See text for details.</p

Transformation matrix for part of the case study (using three Affymetrix CEL files and three sequencing result files for the same kidney sample [<b>21</b>]).

<p>Experiments are displayed as rows, transformations as boxes with color indicating grouping of the transformations. Final data properties are displayed on the right side. Transformations can be added, removed and configured using context menus.</p

Examples of predicted ncRNAs: genomic context, tiling array pattern and predicted consensus structure

<p><b>Copyright information:</b></p><p>Taken from "Comparative analysis of structured RNAs in indicates a multitude of different functions"</p><p>http://www.biomedcentral.com/1741-7007/5/25</p><p>BMC Biology 2007;5():25-25.</p><p>Published online 18 Jun 2007</p><p>PMCID:PMC1914338.</p><p></p> The color scheme used for coloring the RNA structures and the mountain plots representation is the same as in Figure 2. (a) and (b) Intergenic region with predicted RNA overlaps with transcripts described by David et al [9]. Note, that in (b) the sequence for sacKud.contig1979/20479-20583 is truncated (a stretch of seven gaps in the 3' end of the stem, which is not compensated by the deletions in the 5' part of the stem), which probably renders an unusable RNA due to an altered secondary structure. (c) Intergenic region with predicted RNA overlaps with promoter associated transcript described by Samanta et al [7]. (d) Predicted H/ACA snoRNA, overlapping with transcripts described by both David et al [7] and Davis et al [8]

Correlation of 'predicted RNA structures' with UTR-regions and TF-binding sites

<p><b>Copyright information:</b></p><p>Taken from "Comparative analysis of structured RNAs in indicates a multitude of different functions"</p><p>http://www.biomedcentral.com/1741-7007/5/25</p><p>BMC Biology 2007;5():25-25.</p><p>Published online 18 Jun 2007</p><p>PMCID:PMC1914338.</p><p></p> (a) Number of 'predicted RNA structures' in intervals of increasing length adjacent to coding sequences. (b) Number of 'predicted RNA structures' overlapping with transcription factor binding sites taken from [18]

Known RNA genes in the yeast genome, covered by predicted RNA structures

<p><b>Copyright information:</b></p><p>Taken from "Comparative analysis of structured RNAs in indicates a multitude of different functions"</p><p>http://www.biomedcentral.com/1741-7007/5/25</p><p>BMC Biology 2007;5():25-25.</p><p>Published online 18 Jun 2007</p><p>PMCID:PMC1914338.</p><p></p> The annotation was taken from the Genome Database. Structured elements with reported values larger than 0.5 (left) and 0.9 (right) are shown

<em>Yersinia pestis</em>: New Evidence for an Old Infection

<div><p>The successful reconstruction of an ancient bacterial genome from archaeological material presents an important methodological advancement for infectious disease research. The reliability of evolutionary histories inferred by the incorporation of ancient data, however, are highly contingent upon the level of genetic diversity represented in modern genomic sequences that are publicly accessible, and the paucity of available complete genomes restricts the level of phylogenetic resolution that can be obtained. Here we add to our original analysis of the <em>Yersinia pestis</em> strain implicated in the Black Death by consolidating our dataset for 18 modern genomes with single nucleotide polymorphism (SNP) data for an additional 289 strains at over 600 positions. The inclusion of this additional data reveals a cluster of <em>Y. pestis</em> strains that diverge at a time significantly in advance of the Black Death, with divergence dates roughly coincident with the Plague of Justinian (6^th to 8^th century AD). In addition, the analysis reveals further clues regarding potential radiation events that occurred immediately preceding the Black Death, and the legacy it may have left in modern <em>Y. pestis</em> populations. This work reiterates the need for more publicly available complete genomes, both modern and ancient, to achieve an accurate understanding of the history of this bacterium.</p> </div

MOESM2 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes

Additional file 2. Mapping statistics of input read pairs mapped to the reference genomes. Sequencing reads derived from the Chinese strain SRA data were mapped to the Treponema pallidum subsp. pallidum (TPA) SS14 and Nichols reference genomes [6] and to the rabbit genome (Statistics was calculated from post-processed mappings; repetitive and homologous sequences and PCR duplicated reads were excluded from the statistics)

dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in <i>Streptomyces tsukubaensis</i> NRRL18488 and general analysis of the transcriptome

<p>FK506 (tacrolimus) is a valuable immunosuppressant produced by several <i>Streptomyces</i> strains. In the genome of the wild type producer <i>Streptomyces tsukubaensis</i> NRRL18488, FK506 biosynthesis is encoded by a gene cluster that spans 83.5 (kb). A whole transcriptome differential shotgun sequencing (dRNA-seq) of <i>S. tsukubaensis</i> was performed to analyze transcription at 2 different time points; before and during active FK506 production. In total, 8,914 transcription start sites were identified in either condition, which enabled precise determination of the 5′-UTR length of the corresponding transcripts as well as the identification of 2 consensus sequence motifs in the promoter regions. The transcription start sites of all gene operons within the FK506 cluster were identified, including 3 examples of leaderless RNA transcripts. These data provide detailed insight into the transcription of the FK506 biosynthetic gene cluster to support future regulatory studies, genetic manipulation, and industrial production.</p

Molecular characterization of <i>Treponema pallidum</i> subsp. <i>pallidum</i> in Switzerland and France with a new multilocus sequence typing scheme

<div><p>Syphilis is an important public health problem and an increasing incidence has been noted in recent years. Characterization of strain diversity through molecular data plays a critical role in the epidemiological understanding of this re-emergence. We here propose a new high-resolution multilocus sequence typing (MLST) scheme for <i>Treponema pallidum</i> subsp. <i>pallidum</i> (TPA). We analyzed 30 complete and draft TPA genomes obtained directly from clinical samples or from rabbit propagated strains to identify suitable typing loci and tested the new scheme on 120 clinical samples collected in Switzerland and France. Our analyses yielded three loci with high discriminatory power: TP0136, TP0548, and TP0705. Together with analysis of the 23S rRNA gene mutations for macrolide resistance, we propose these loci as MLST for TPA. Among clinical samples, 23 allelic profiles as well as a high percentage (80% samples) of macrolide resistance were revealed. The new MLST has higher discriminatory power compared to previous typing schemes, enabling distinction of TPA from other treponemal bacteria, distinction between the two main TPA clades (Nichols and SS14), and differentiation of strains within these clades.</p></div

Allelic variants of all available strain sequences for TP0136, TP0462, TP0548, TP0705 and TP0865.

<p>Alleles found in 120 clinical samples examined in this study (samples from France and Switzerland) and in 63 samples published in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200773#pone.0200773.ref024" target="_blank">24</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200773#pone.0200773.ref025" target="_blank">25</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200773#pone.0200773.ref036" target="_blank">36</a>] (total n = 183) are shown. <b>A. Structural arrangement of candidate loci on the genome.</b> The TP0705 and TP0865 genes lie on the complementary DNA chain. <b>B. Allelic variants</b>. Sequence alignments show only positions containing nucleotide variants. Numbers correspond to nucleotide positions in TPASS_0136, TPASS_0462, TPASS_0548, TPASS_0705, TPASS_0865 genes (TPA SS14; CP004011.1) or to TPANIC_0136, TPANIC_0462, TPANIC_0548, TPANIC_0705, TPANIC_0865 genes (TPA Nichols; CP004010.2). Deletions are shown with dashes or “del”. Allele variants that were found among clinical samples in this study (clinical samples from France and Switzerland) are shown in red. For TP0136 and TP0548, the sequence variants were translated to both current molecular typing systems (SBMT and ECDCT) and new sequence variants, which were not identified in previous typing studies, are shown in red. Sequence variant TP0136_11 represent TPA strain Dallas (DAL-1), which contains 30 SNVs and a 58 bp long deletion in TP0136 locus.</p