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Further, the splitting of TIs as part of alignment pre-transition uncovered an underlying imbalance in the capacity of different HRGs that had not been observed before, with MSM/TG TIs generally weaker than FSW TIs.
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As with the identity-based tests, trailing 'A' residues that were part of alignments were trimmed prior to computing the statistics.
This removal of hypervariable regions is conducted automatically as part of the alignment procedure of the RDP alignment algorithm [ 24], which allows for tidy comparison of sequences with the same number of positions, but also may eliminate valuable information.
For a given family, each of the proteins studied here was aligned separately to the original Pfam alignment (unless it was already part of that alignment).
Our preanalyses showed that dubious sequences or ambiguous parts of alignments had much greater effect on the outcome than selecting taxa with the highest amount of data available.
If so, how do we know whether in this case the upper part of the alignment is not in fact the bottom part of the alignment of another family shown above?
If it is found to be contained in one of them, the candidate sequence is aligned by simply copying the matching part of the alignment of the reference sequence.
Clustering and tree structures are used as part of the alignment algorithms, as well as for the processing and representation of the alignment results.
The distance required to perform this maneuver, known as the sight distance, is an integral part of highway alignment.
Route 27 was part of the alignment through New Jersey of the Lincoln Highway, the United States' first transcontinental highway that was established in 1913.
Prior to construction of Route 133, Route 92 was to follow part of its alignment around Hightstown before turning northwest and continuing beyond U.S. Route 1 to U.S. Route 206 and the never-built Somerset Freeway (Interstate 95).
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