Usually, one considers both orientations of the sequence or equivalently both PWM orientations.
In our effort to identify the effector mechanism directing Pc-G proteins on the targeted sensor transgene, we found that the silencing machinery active in the soma has the capacity to discriminate between both orientations of the Idefix sequence present within the sensor transgene.
This allowed the identification of the nature and orientation of sequences present at the breakpoint relative to the parental chromosome sequences allowing prediction of the structure of the resulting rearranged chromosomes.
The orientation of sequences was also derived from BLAST annotations.
Many of the gaps are unbridged, representing spaces in the genome build of unknown length, and importantly, the relative orientation of sequences on either side of these gaps are also unknown.
We consider the problem of using optical maps to determine the relative placement and orientation of sequence fragments produced during the assembly process (scaffolding).
Genetic linkage maps represent a key resource to understand genome organisation, evolutionary relationships, and to assist in the assignment and orientation of sequence assemblies to correct chromosome locations.
The effort required for establishing the order and orientation of sequence contigs--a key part of the sequence-finishing process--directly relates to the number of uncaptured gaps in the sequence assembly.
Comparative-grade finished sequence is produced by establishing the order and orientation of sequence contigs greater than 2 kb in size, and then independently verifying the resulting sequence contig map by auxiliary data.
Furthermore, this high-density map should aid in genome sequencing analysis in Arachis spp., because the locus order can work as a reference for the orientation of sequence contigs and scaffolds.
Thus, with respect to the ability to establish the order and orientation of sequence contigs relative to one another, the GS FLX assembly was comparable to a Sanger-based assembly.
