Second, as described in Additional file 2: Note 1, two regions, one approximately 10 kbp and the other approximately 8 kbp, were amplified, sequenced with the Sanger method and aligned to the genome.
Third, we found that vector DNA fragments that were captured by selective hybridization, sequenced by the Sanger method and aligned to the vector were of the approximate length of a nucleosome core DNA at both the 3-day (mean ± SD 146 ± 14.4 bp) and 6-week (146 ± 16.0 bp) time points.
The same genomic DNA sample of E. coli strain DH1 ME8569 was sequenced using these three sequencing methods, and aligned to the reference.
These soft trimmed mates were identified (described in methods), and aligned via BLAT to hsBuild-37.1, revealing the deleted region to be of length 11,020 bases, located on chr5, between bases 112,034,824 and 112,045,845, spanning the annotated APC promoter 1B.
Expression of the putative PRAMEY loci was investigated by deep-sequencing of the selected testis cDNAs using the Illumina GAIIx (see methods) and aligning the short sequence reads (pair-ends, 2×36 bp) against unique coding regions of the PRAMEY genes (Table S2).
Sequences were aligned with published OPV sequences in GenBank by using the ClustalW (www.clustal.org/) method and manually aligned by using MEGA version 4.0 (Arizona State University, Phoenix, AZ, USA).
To evaluate these calls in the absence of ground truth, we assembled predicted calls for all methods using TIGRA and aligned the resulting contigs with the BLAST-like alignment tool (BLAT) (Kent et al., 2002).
We used sequences from published patent claims in the Cambia patent database (see Methods and data) and aligned them to the human CCDS gene set using the Basic Local Alignment Search Tool BLASTT).
More recently, different groups have used chemical vapor deposition method and prepared aligned carbon nanotubes (ACNTs) [17 23].
The procedure to couple the roughness noise sources to the tailored Green's function is detailed for the case where the boundary element method mesh is orthogonal and aligned with the boundary layer outer velocity.
Because so many different smoking machine and exposure systems are used, it is clear there needs to be a simple and aligned method of measuring dose in vitro; this is especially the case with the current switch from liquid to ALI exposures of aerosols in vitro [ 16].
