The order and orientation of contigs within Hi-C scaffolds were determined based on contact frequency calculated from mapped Hi-C read pairs.
The order and orientation of most BAC clones in each contig were confirmed by BAC-end sequencing.
However, the order and orientation of DNA sequences within BACs is often not known.
Mate pair information was used to predict the order and orientation of the contigs, confirming that no genomic rearrangements were present relative to KIM 10+.
In chicken the order and orientation of the genes remains unchanged and they are integrated with genes which represent the main part of X conserved regions in mammals.
By mapping markers at both ends of the short linkage contigs, the order and orientation of these contigs are rapidly assembled in the long range physical linkage maps.
In contrast, the ANT-C cluster of Drosophila contains multiple genes between Hox genes, and the transcriptional orientation of Dfd and ftz is reversed with respect to the order and orientation of other genes within the complex [7].
Therefore, the sequence of this strain was used as a scaffold to determine the order and orientation of the contigs for further DNA sequencing of the gaps between the contigs.
However, the order and orientation of the contigs was unknown.
The order and orientation of the FPC contigs were examined by aligning on the shotgun scaffolds.
The order and orientation of some genes within each cluster type was conserved.
