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pan-genome size might be affected by sequencing additional phylogenetic groups.
The reason is that long open reading frames are likely to be affected by sequencing errors in form of in frame stop codons.
Since these redundant reads may also be affected by sequencing errors, they may increase the dimensionality of the data, further reducing the efficiency of the assembly process.
This result suggests that SNPs with high MAF (e.g. 40 50%) are less likely to be affected by sequencing errors and thus, should be given high priority during marker development.
However this technique only applies to larger events and can be affected by sequencing biases.
In silico maps could also be affected by sequencing or assembly errors [ 10], but these are less likely to affect alignments because typically they are infrequent.
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Since direct pattern search is affected by sequencing errors, e.g., insertions/deletions, we implemented a Smith-Waterman algorithm using MatLab (Natick, MA) running on the DEAC computer cluster at Wake Forest University.
It was suggested by Lindsay et al. (2008) that codon models used to estimate ω might be affected by sequence composition.
There is a risk that the methylation differences detected by the MeDIP technique could be affected by sequence differences in the promoter regions used for the arrays.
In addition, break points may be affected by sequence composition, with GC-rich regions appearing to be particularly susceptible to breakage [ 2].
Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database.
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