Another method which does not require time alignment as a pre-processing stage is the iterative combination of a nearest neighbour search step and a conversion step alignment method (INCA) [12].
For this reason, we employ the use of a DTW-based distance measure, which does not require temporal alignment nor synchronization between a pair of sequences in different sizes [11].
Contig pairs with a single alignment which does not extend over the full length of the shortest contig may represent different genes which share a conserved protein domain.
This may be unimportant for the C-MAC, which does not require the alignment of the oral, pharyngeal, and tracheal axes to visualize the glottis [ 2].
Notice that the alignment between the two trees maps the intervals in a manner that preserves the tertiary structural information and the other information surrounding the loops - thus exemplifies a biologically verified alignment which does not preserve branch ordering.
This benefit may be explained by the pronounced curvature of the Airtraq blade, which does not require the alignment of oral, pharyngeal and tracheal axes, and the disposition of its optical components, allowing intubation in patients with reduced mouth opening.
We then used the RNA22 algorithm (http://cbcsrv.watson.ibm.com/rna22_targets.html) [27], which did show alignment of the putative seed region within the UTR.
Based on these results and the works of others, we propose an algorithm which does post-processing on alignments output by HMMs to automatically recognize vowel length.
Here we approached these issues using a profile-based method for proteins grouping, which does not base on alignments.
The text is well written and the advantage of JSAV over other tools becomes clear: It is a simple Java script library for basic alignment visualization which does not require any other server program.
