The phrase "alignment to repetitive" is not correct and does not convey a clear meaning in written English.
It may be intended to describe a relationship or connection to something that is repetitive, but the phrasing is awkward and unclear.
Example: "The alignment to repetitive tasks can lead to burnout if not managed properly."
Alternatives: "connection to repetitive" or "relation to repetitive".
However, there are several limitations inherent to the alignment process, including alignment to repetitive regions, absent or misassembled sequence in the reference genome, and individual genetic divergence between the subject organism's genome and the reference genome [ 1].
Sequences that had any local alignment to repetitive sequence were discarded.
Closer examination of the IAS pipeline revealed that the Bowtie2 alignment tool was reporting alignments to repetitive regions that could not be uniquely mapped.
Alignment of the unisequences to repetitive elements in RepBase release 14.08 [ 74] was done with BLASTN that was automated using in-house Perl scripts (available upon request).
This program efficiently uses the information obtained from paired-end reads to correct alignments and accurately map short reads to repetitive sequences.
Note that application of some form of repeat masking is necessary to keep a local alignment tool of choice from being overwhelmed with hits to repetitive genomic segments.
No changes in cell shape or the direction of cell alignment were observed, as has been reported for cells exposed to repetitive cycles of pure uniaxial compression [26].
Current analytical methods mostly rely on sequence alignment against a unique reference genome, and unspecific mapping of short reads to repetitive regions is problematic with many events mediated by repetitive elements potentially being missed (Conrad et al., 2010a).
Thus, large stretches of unread sequences are likely to arise from three possible situations: First, since the 'galign' alignment tool assigns all repetitive sequences to the first occurrence of the sequence in the genome, and repeats occurring more than four times in the genome are ignored, large unread stretches could correspond to repetitive domains of the genome.
Methods such as RECON [ 17] utilize whole-genome alignments to identify repetitive elements de novo.
The absence of any alignments to known repetitive sequences also hints that RAD markers are clustered within recombinatorially active regions of the genome.
