Although BLAT alignments generate uninterrupted representations of the aligning regions, one drawback of BLAT when performing alignments of evolutionarily distant DNAs, as initially noted by Kent [ 6], is that short regions of homology that span the non-overlapping 11-mers go undetected.
To ensure an uninterrupted data flow, auto-alignment transmitter and receiver modules are necessary [12, 17, 18].
We defined regions of sufficient sequence similarity for unambiguous alignment (called common uninterrupted regions or CURs, see " Methods"), which altogether covered ~8.5 Mb of the 12 Mb genome.
Unlike other multi-genome comparative tools that display columns of aligning bases with gaps to optimize alignments, EvoPrinter displays, in a single uninterrupted view, DNA sequences that are either conserved, unique or uniquely shared, including single nucleotide polymorphisms (SNPs), as they exist in the genome or MGE of interest.
The best alignment could be the one with continuous helix or strand uninterrupted by gaps in the alignment.
The longest uninterrupted open reading frame that overlapped with the tBLASTx alignment was used for further analysis.
Generated from superimposition of multiple pair-wise BLAT alignments [ 6], an EvoPrint provides an ordered uninterrupted representation of conserved sequences as they exist in the genome of interest.
In order to obtain high precision in the estimation of the substitution frequency, we eliminated from the analysis any windows containing concatenated alignments that had less than 100 kb of uninterrupted unambiguous nucleotide sequences (no indels and no N bases) (Duret and Arndt 2008).
The ASD is described as the uninterrupted line of sight between the driver's eye and the obstacle, and depends mainly on the alignment configuration as well as the various sight obstructions due to constructional elements or equipment of the roadway (backslopes, barriers, walls, etc).
Uninterrupted, yes, but not unbiased.
Few achieve such uninterrupted progress.
