We speculate that CREST fails at the BLAT alignment stage, because small novel sequences complicate the alignment results.
Low complexity and repetitive regions are common in the human genome, which complicates the alignment of short sequencing reads.
The X. tropicalis sequence was not included in this analysis because its unique Otop family expansion complicates the alignment of non-coding sequences with other species' sequences.
As expected the average identity also drops slightly (2.8 2.9%) because with increased length of the assembled sequences, internal sequence variations accumulate and complicate the alignment of the extended contigs against the target genome.
The high evolutionary rates of rodent introns can complicate the alignments, phylogenetic reconstructions and measurement of genetic distances.
This provides an accurate estimate of false positives and aids in the identification of paralogous regions that complicate the alignments between FPC contigs and genetic markers, since the size of the PCR products from paralogous regions may be identical.
In nine cases (one in the motif-free set and eight in the motif-containing set), the presence of indels not verified by ESTs or a high variability, both in the very 5' end of the gene sequences, complicated the local alignment.
The location of three of the four teams in the East complicated the divisional alignments, so the governors adopted a rotating system that has little regard for geographic location.
The image scaling resulted in a decrease in image size (both optic resolution and digital resolution as compared to the original image), which would complicate the data alignment issues.
Furthermore, the high level of noise present in the PET images, coupled with possible residual motion artefacts and attenuation artefacts [10], might complicate the perfect alignment of the two datasets and therefore increase the chances to introduce additional, anatomy-driven artefacts in the PVC-PET reconstructions.
