Additional file 12 of A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis

Taxon assignment of HMP-mock2. Taxa were assigned to OTUs resulting from sl1p’s options for OTU clustering, taxon assignment, and choice of reference database. Resulting taxa was compared to the known composition of the community to determine correct taxa assignment. (PDF 153 kb

Additional file 6 of A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis

Outline of reads lost in the URTCul dataset during sl1p’s quality control pipeline. More input reads were culled during the PANDAseq alignment step in this dataset compared to HMP-mock (Fig. 3), possibly due to a difference in target variable region length between the two datasets. (PDF 55 kb

The expression profile of the rpoS gene.

<p>The turn point is the half position from lift maximum, the turn off point is the half position from the right maximum.</p

The mapping of unknown condition based on pattern matching of expression.

<p>For example, the expression pattern in the complex media of sputum extracts looks most like minimal media growth conditions. The clustering analysis of the expression data for the 72 conditions can yield groups of conditions with similar expression profiles, which can be used for pattern mapping of unknown condition based on expression pattern mapping.</p

The environmental conditions tested.

<p>The environmental conditions tested.</p

Pattern matching of temporal data.

<p>A. This is an original similarity matrix from PCA similarity analysis, the deep red on diagonal is similarity of itself, the similarity is 1. B. This is the reorganized similarity matrix based on clustering analysis.</p

The list of the gene reporters used in this study.

<p>The list of the gene reporters used in this study.</p

The <i>aprA</i> gene expression profiles in 72 conditions and 60 time points.

<p>The <i>aprA</i> gene expression profiles in 72 conditions and 60 time points.</p

The Gene Activation Order in the Networks.

<p>The Gene Activation Order in the Networks.</p

Expression Profiles of the 31 Genes in One Condition.

<p>Expression Profiles of the 31 Genes in One Condition.</p