For instance, a structurally correct alignment is an alignment where aligned residues play similar role in the 3D structure.
Performing a global alignment where the aligned symbols are the exons, there cannot be internal gaps (missing exons) and aligned exons must have the same phase.
This was compared with an alignment where ambiguously aligned positions had been identified by eye; the two alignments were almost identical and yielded identical phylogenetic estimates.
To measure correctness, we compute Smod, the ratio of the number of correctly aligned positions to the number of aligned columns in the evaluated alignment where at least one of each two aligned columns is present in the reference alignment.
The initial state in this iterative routine corresponds to a rough alignment where micrographs are aligned by means of simple cross-correlations.
We use two different score evaluation parameter sets for the forward alignment (where the two back-translated graphs that are aligned have the same translation sense) and the reverse complementary alignment (where one of the graphs is aligned with the reverse complementary of the other), because these are two independent cases with different score distributions.
Prior to phylogenetic tree calculation, non-aligned ends have been trimmed and all portions of the alignment where a substantial number of sequences contained gaps have been removed.
Furthermore, CUSHAW2 is on an average superior to all other evaluated aligners in terms of both recall and precision for the SE PEE) alignment, where the average recall is ~89.92% (90.75%) and the average precision is ~97.46% (98.28%).
In [ 22] we used the BALISCORE, which computes the fraction of identities between a trusted reference alignment and a test alignment, where identity is defined as the averaged sequence identity over all aligned pairs of sequences.
But analysts and Microsoft competitors offered a mixed view on whether there had been any shift in an industry alignment, where Microsoft has been a clear No. 3 until now.
In my view, it does not mean that the United States has suddenly decided to return to a pre-1979 alignment where Iran is one of our principal allies in the region.
