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The whole alignment process is verified by calculating the RMSD between aligned and nearest template coordinates.
These cases are largely an expression of comparisons between unaligned sequences; however, in some instances a part of the CDS or NCS aligned well but constituted only a minor fraction of the whole alignment, producing a value below 0.25.
We also studied the whole alignment results for comparison.
The whole alignment X is assumed to be decomposed into K consecutive segments.
The knowledge of even one 3D protein structure in a given sequence alignment provides a powerful means to test the correctness of the whole alignment.
Many techniques are based on sliding window procedures that compare the topology of one segment against neighboring segments or the whole alignment.
Similar(21)
ANOVA was performed to test variation in branch lengths of whole alignments or 3-kb nonoverlapping windows between and within autosomal chromosomes in cattle, dog, and human.
A lower-scored whole ITS alignment was also examined (Alignment S3).
Blastz [ 16] is a pairwise whole genome alignment method, which produces local nucleotide sequence alignments.
They are accustomed to studying wide-angled game film, to seeing the whole defensive alignment and the entire routes of the receivers.
Full simulation of the whole CMS alignment system, with over 30,000 parameters, is quite advanced.
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