A current limitation of the alignment-free methods is that after a set of sequence signatures are found to be discriminative for the classification, the biological indication of these k-tuple features is still not clear.
Reads from the PrCa sample were trimmed to 50 bp from 75 bp to meet technical limitations of the alignment program.
Therefore, in this study, alignment parameters were optimized and a post-alignment filter was applied to overcome the above limitation of the global alignment algorithm.
Hence, by combining both techniques, the limitation of the sequence alignment method can be solved.
Due to the limitation of the sequence alignment method, the feature selection method was introduced in [ 9] to predict the remaining sequences.
Hence, one of the limitations of the pairwise alignment is that the query sequence is restricted only to apicomplexa, therefore, the query and subject proteins should not be reversed in their order.
First, many two-phase methods (first align, then compute a tree) simply fail to run on very large datasets (Liu et al., 2010), largely because of limitations in the alignment methods.
Whilst it is not advisable to fit a parameter rich REV model in practice, due to computational constraints and uncertainty in parameter estimates on small alignments, we should aim to derive the best model, given the limitations posed by the size of the alignment.
The D/E/N/Q mis-alignment within the RIP family of proteins is representative of a more general limitation of structure alignment programs.
Another limitation of targeted alignment in this study is that we restricted our analysis to readthrough fusions across adjacent genes on the same genomic strand.
