The right eye of subject 2 depicts the largest isoplanatic patch and indicates using the LOS wavefront reference arrangement would be suitable for wide field imaging in this eye.
The gap closure was supported by the related reference contig arrangement tool r2cat, using the complete C. jeikeium K411 genome sequence as a reference [ 21].
The gap closure process was supported by the related reference contig arrangement tool r2cat, using the C. diphtheriae NCTC 13129 genome sequence as a reference [ 13].
Although in each case several sequence reads supported the detected polymorphism, these regions were also covered by paired-end reads that supported the Nipponbare reference genome arrangement.
The remaining gaps were closed by a PCR strategy that was supported by the related reference contig arrangement tool r2cat [ 13], using the Corynebacterium diphtheriae NCTC 13129 genome sequence as a reference [ 14].
In this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in the task of comparative assembly and also provides an interactive visualization for synteny inspection.
Our program r2cat (related reference contig arrangement tool) is able to quickly match a set of contigs onto a related genome, order the contigs according to their matches and display the result in an interactive synteny plot.
The resulting reads were assembled with the Newbler Assembler software, and the remaining gaps were closed by PCR strategies that were supported by the related reference contig arrangement tool r2cat [ 26] using the genome sequence of C. pseudotuberculosis FRC41 as a reference [ 21].
The subsequent gap closure process was facilitated by in silico predictions of the contig order that were computed by the related reference contig arrangement tool r2cat using the C. pseudotuberculosis FRC41 genome sequence as a reference and the default parameters of the integrated q-gram filter [ 21, 26].
Ten DGRP lines identified with the y; cn bw sp; reference genome arrangement of Cyp12a4 and Cyp12a5 (456, 45, 239, 639, 101, 40, 491, 440, 42, and 228), and eight DGRP lines with the Cyp12a4/5 chimeras arrangement (358, 399, 217, 365, 129, 443, 705, and 357), along with the lufenuron-resistant strain NB16 (Bogwitz et al. 2005), were raised on rich media and placed in mass-bred cages.
