ANN-based NetMHC/NetMHCII 40, 41 and NetMHCpan/NetMHCIIpan 42, 43 took advantage of alignment-based NN-align or similar processes 41, 66 to get both the 9-mer cores and the peptide flanking residues for Class II HLA binders.
Of course, one distinct advantage of alignment-based methods is their faster running time, especially for ungapped alignment (see Table S1).
Reviewer's report 3: Prof J. Peter Gogarten (University of Connecticut, USA) Chan and Ragan provide a concise review of the advantages of alignment free approaches in comparative genomics.
Other advantages of alignment-free genome comparison are that they can work with unassembled reads (Song et al., 2012) and are not affected by genome rearrangements.
We took advantage of 4,677 alignments covering a total of 9.78Mb of human, chimp, and baboon non-coding DNA curated by Julien Meunier [12].
FastBLAST avoids most of the work of all-versus-all BLAST by taking advantage of these alignments and by clustering similar sequences.
This effect illustrates the advantage of clustering alignments in contrast to clustering the expression profiles directly.
It is determined that a device designed to have a large clear aperture of 15 μm would have an advantage in terms of alignment.
In the spirit of creative fragmentation, why not take advantage of the chance alignment of unrelated recordings to traverse the "Ring" (three-fourths of it, anyway) in contrasting readings, all live, all unfamiliar?
The players association, however, has submitted an idea for two leagues of 15 teams each, with Houston moving to the A.L. The advantage of the 15-15 alignment would be that the leagues and their avenues to the playoffs would be symmetrical -- three divisions of five teams each with three division champions and a wild card for the playoffs.
Then, by taking advantage of signal level alignment of the interference from different users, we generalize the scheme to multi-user cases.
