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The reason for this changing is to keep alignment with the structure of the MSE transfer chart for BP-based iterative channel decoding and state estimation.
These were also surrounded with packs of sausages and re-placed on the motion table as in a patient acquisition procedure, with no attempt to keep alignment orthogonal by any other means than manual placement.
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To keep the alignment of SiC NFs, the optimized spinning time is 5 min.
Make sure to keep the alignment pin in its hole as you put the new pump in place.
Perform local alignment between the genome and each read individually, and keep alignments that have score higher than a threshold.
The disruption of the ND5 sequence precluded using it in our analyses and for consistency the entire gene was excluded to keep all alignments comparable.
To equalize results, we applied an external filter to keep only alignments greater than or equal to 50 bp in length, and ran each aligner with its thresholds set so that such alignments were not filtered out internally.
A full-length multisequence alignment of all the Msx orthologs and paralogs was facilitated by the identification of the conserved Msx Homology domains, as highly conserved amino acids within MH domains (MH1N and MH2) were used as homologous landmarks to keep the alignments in register (see Methods).
When such alignments need to be extended, e.g. after new sequences become available, it may be preferable to keep the relative alignment of existing sequences intact and have the new sequences aligned to this reference alignment.
Instead of attempting to recover all possible alignments for each short read, we chose to keep only one alignment for any read that matched to the database, so that the final counts accumulated along a "consensus" element for each repeat type, though the reads could align to many instances of that repeat in the genome.
However, this constraint is too tight because it forces all sequences in the subtree to keep the same alignment with the remaining sequences, and may not include any alignments consistent with τ'.
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