The program finds fragments in the alignments that were likely to be recombined, either inside the alignment (global inner fragments, GIs) or with another sequence (global outer fragments, GOs).
For each significant outer hairpin loop pair, the optimal structure alignment of inner elements is computed.
For each significant outer hairpin loop pair, the optimal structure element alignment of inner elements is computed.
To compute a similarity score, limited alignment without inner gaps and with limited maximal number of trailing gaps is performed.
Here, gaps are allowed in the local alignment of inner structure elements; however, no gap penalty is used.
First, we visually compared alignments for congruence in their ability to align sections of the alignments (especially the inner core) using AltAVisT [54] and the overall sequence identity calculated from each alignment.
The film is about Lili's "transition", the process (the production notes tell us) that "trans people undertake to bring their body and their gender expression into alignment with their inner gender identity".
In my case, I became so uncomfortable with the central fact of my existence — my younger brother, alone in an Albuquerque apartment, at the age of twenty-two, choosing death over life — that I had to find ways to perpetuate the discomfort day-to-day in order to feel comfortably uncomfortable, to bring my external reality into alignment with my inner life.
4. Are they out of alignment with their inner gods and goddesses? 5. Do they suffer from Narcissistic Personality Disorder?
This sense of inner alignment is often referred to in the worlds of psychology and personal development as having integrity or being authentic.
