Exact(6)
In contrast, the ILP needed 9.6 min for all alignments in the MassBank datasets and 14.5 min for all alignments in the Orbitrap dataset.
All alignments in the test set were used as positive test cases and their realigned reverse complements as negative test cases.
Calculating all alignments in a consistent direction with respect to the reference read produces a more accurate multialignment, particularly near homopolymer runs.
We filtered all alignments in a consistent manner across each set of species using several criteria that could be applied in each clade considered.
All alignments in these panels are performed relative to the backbone atoms of residues 85 92 (the P-loop) in our no-nucleotide structure (shown in (C )).
More specifically, we run a banded version of the forward algorithm by [ 13], considering all alignments in a band of size three around a guide alignment produced by BLASR.
Similar(54)
Table 6 gives the number of correctly aligned residues across all the alignments in each sequence identity bracket.
All alignments used in this study are available in Nexus format upon request of DWR.
All alignments used in this study were deposited in DRYAD (accession no. doi: http://10.5061/dryad.14214).
First, all 13 Rickettsia sequences were aligned (all alignments are shown in Figure S9).
All alignments used in this study have been provided separately.
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