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In Figure 2 the genomic range spanned by persistent genes is plotted for all the 113 genomes.
We were interested in estimating the genomic range in which local regulation is observable.
However, it is difficult to determine the genomic range of cis-acting for lncRNAs.
Thus, the shortest possible genomic range covered by persistent genes was always found.
Thus, if the region of intersection was a square, the localization would give the genomic range allowed for each breakpoint.
The genomic range of respective genes was determined according to the Ensembl transcript and Genscan predictions (Additional file 3).
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Lawrence, M. et al. Software for computing and annotating genomic ranges.
Then GenomicFeatures, Genomic Ranges and GenomicAligments R libraries were used to count the number of reads with respect to the annotation reference.
These genomic ranges will be referred to hereafter as loci.
This is reasonable, as the genomic ranges analyzed here are <200 bp.
These variants can affect single nucleotides or larger genomic ranges by substitution, insertion, deletion, or change in copy number.
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