An additional drawback is that using only the single center of mass point in each projection removes the use of any local structure of the projections as criteria for alignment.
To verify that we could reproduce the results of Ref. [ 9], we relaxed our criteria for alignment length to 70%, thereby increasing our dataset to 870 sequence-structure pairs.
In either case, it is clear that alternate criteria for alignment may be called for depending on whether a method is being applied to regions defining the structural core of a protein vs. regions elsewhere, for example.
We applied stringent criteria for alignments.
Both algorithms use the heuristic FASTA comparison strategy to accelerate the search but use alignment probability, rather than similarity score, as the criterion for alignment optimality.
In addition, we used the column score where the percentage of correct columns in an alignment is the criterion for alignment quality.
However, if the similarity criterion for alignment was less stringent (90%), 653 primer pairs were virtually transferable between at least two species.
Secondly, with stringent filtering criteria some BPs may be missed, illustrating that the use of flexible filtering criteria for MPS alignment might be helpful.
In a single run, a total of over 10 million short sequences were obtained, and 9 237 194 were selected by quality control criteria for the alignment.
Moreover, to reduce the problems of misalignments, local realignment of reads with InDels have been suggested and to minimise the detection of false positives due to other factors, stringent criteria for post-alignment filtrations needs to be applied [ 25].
The BLAT program was used to extract from the PN40024 genome a total of 1709 copies paralogous to the 13 canonical copies representing the families identified in this study at the most stringent criteria for seeding alignments based on sequences of 95% and greater similarity over 40 bases of length or more.
