Sentence examples for identically aligned from inspiring English sources
The agreement of a given alignment, S, with the reference alignment, R, is defined as the percentage of the residue pairs in the alignment which are identically aligned as in the reference alignment (I S ) relative to the reference alignment's length (L R ), i.e., A S, R) = (I S / L R ) × 100.
The large number of positions not identically aligned between the three alignments made us confident that the alignment space investigated was not too narrow.
Ambiguously aligned regions were excluded using GBlocks (Talavera and Castresana 2007) and double-checked with HoT (Landan and Graur 2007), retaining positions that were identically aligned in the reverse and forward alignments.
I0 is the number of identically aligned residues in the reference and the method alignments; I1 is I0 plus the number of aligned residues that are shifted by one position, and so on.
Considerable parts of the ITS were not identically aligned between these three approaches, including a very long alignment-ambiguous part of the ITS1 and two shorter alignment-ambiguous parts of the ITS2.
For each read-alignment, we calculated two numbers: mapLength: the ratio of the number of aligned bases and the read length; and mapQuality: the fraction of identically aligned bases, averaged over all exonic blocks of the read-alignment.
It is calculated as the ratio of the sum of scores p for all pairs of residues in every column of the alignment by the sum of scores in the reference alignment; p?=?1 if the pair of compared residues is aligned identically in the reference alignment, otherwise p?=?0.
The TC score is calculated considering the ratio of the sum of scores c by the number of columns in the alignment, being c?=?1 if all residues in the column are aligned identically in the reference alignment, otherwise c?=?0 [ 20].
The three alignments were compared using SOAP [74], and only positions that were aligned identically among them were included in phylogenetic analyses.
Protein sequences were identified and aligned identically for all four Symbiodinium clades.
We labelled as cross-platform "target matches", sets where the oligonucleotide sequence of a probe aligned identically to the sequence spanned by all probes of an Affymetrix probe set.
