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Interestingly, PGA Tour players, who you wouldn't expect to have this problem, routinely use alignment aids when they are on the practice range.
Instead, we use alignment rates to estimate the accuracy of error correction.
The Promomer tools use alignment of sequences of genes and enumerative method to find motifs.
Similarly, in the present work, we do not use alignment techniques or any sequence information in our method, relying only on structural grounds.
To estimate the average divergence between Neandertal and human DNA sequences, we use alignment positions in which the human and chimpanzee genomes differ.
This is because these algorithms use alignment methods to search for orthologs that cannot incorporate the large introns contained in the Dscam genes, especially as they are interspersed with short exons.
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We have previously shown (Kantorovitz et al. 2009; Kazemian et al. 2011) that when "training CRMs" from a particular regulatory network are available, this approach is superior to or as effective as existing motif-based methods (Frith et al. 2003) and other methods that use alignment-free scores of sequence similarity (Arunachalam et al. 2010).
More specifically, in order to achieve high computational efficiency, we do not use alignment-based techniques as done e.g. in deepBlockAlign (Langenberger et al., 2012), and we do not resort to a set of handcrafted measurements or features to describe the entire profile as done e.g. in DARIO (Fasold et al., 2011).
The FootPrinter Motif Discovery software [ 18] does not use alignments as input.
Thus, this study guided us to obtain an alignment for generating Model 2 (using alignment in Fig S2B).
Without using alignment thresholds, more than 99.9% of all sequences could be aligned back to the reference.
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