109 research outputs found
Comparison of heterogeneous positions identified in TPA SS14 strain by Matějková et al. [14] and by the automated pipeline used in this study.
<p><sup>a</sup>additional intrastrain heterogeneous genome positions identified by Matějková et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref014" target="_blank">14</a>] including 135141, 135144, 135149, 135220, 135227, 671982, 672004, 672016, 672025, 672026, 672027, 672028, 672036, 672039, 672040, 672041, 672042, 672043, 672044, 672154, 673088, 673119, 673511, 673545, 673550, and 673554 (according to the CP000805.1) were located in paralogous regions and therefore were excluded from the automated pipeline (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.s002" target="_blank">S2 Table</a>)</p><p><sup>b</sup>numbers in parentheses show numbers of sequenced clones [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref014" target="_blank">14</a>] or nucleotide frequency within individual Illumina sequence reads (this study); NA—not available</p><p><sup>c</sup>not present in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.t002" target="_blank">Table 2</a>; heterogeneous positions were detected in raw Illumina sequencing reads but were excluded due to study criteria</p><p><sup>d</sup> these heterogeneous sites were not found among Illumina reads, but were identified among 454 reads (SRX000109)</p><p><sup>e</sup>see also <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.t003" target="_blank">Table 3</a>; independent DNA preparations showed clear differences in proportions of alternative alleles, ranging from 0.1 to 0.7</p><p>Comparison of heterogeneous positions identified in TPA SS14 strain by Matějková et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref014" target="_blank">14</a>] and by the automated pipeline used in this study.</p
Data analysis workflow.
<p><b>(A)</b> An automated identification pipeline and optimization process. <b>(B)</b> An application of further restrictions and verification of identified putative candidates.</p
Viruses detected by sequencing that were not screened by PCR.
<p>The bars represent the number of samples in which each virus was detected by sequencing. *Indicates viruses that were not assayed by PCR in NP samples. **Indicates a virus that was not assayed by PCR but belongs to a genus with members that were.</p
Comparison of sequencing results with Ct values from real-time PCR assays.
<p>The average Ct values from real-time PCR assays for (A) adenovirus and (B) bocavirus are graphed. Each PCR experiment was repeated at least twice per sample. Samples are grouped from left to right according to whether they were detected by sequencing, not detected by sequencing, or only detected when the number of sequence reads was increased to 21 or 51 million sequences for A and B, respectively.</p
Summary of the intrastrain variable sites identified within Illumina sequencing reads in investigated treponemal genomes.
<p>Illumina-identified intrastrain variable sites were verified using 454 or Sanger sequencing.</p><p><sup>a</sup>no intrastrain heterogeneous site were identified in the TPA Mexico A, TPE CDC-2, TPE Gauthier, TPE Fribourg-Blanc and TPLC Cuniculi A genomes</p><p><sup>b</sup>nonconservative amino acid replacements are not listed</p><p><sup>c</sup>if not indicated, localization was predicted by PSORTb</p><p><sup>d</sup>not applicable</p><p><sup>e</sup>[<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref020" target="_blank">20</a>],[<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref023" target="_blank">23</a>]</p><p><sup>f</sup>variable number of direct repeat (TCCTCCCCC)</p><p>Summary of the intrastrain variable sites identified within Illumina sequencing reads in investigated treponemal genomes.</p
Comparison of sequencing and PCR results.
<p>The number of samples in which each virus was detected by PCR (white bars), sequencing (gray bars), or both (black bars) is shown.</p
Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children.
<p>Analysis of 176 plasma and NP samples on the Illumina GAIIX and HiSeq 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.</p
Genome coverage.
*<p>Full genome sequence not available. Largest Genbank sequence used.</p
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