The phrase "alignments in the first" is not correct and lacks clarity in written English.
It may be used in contexts discussing order or sequence, but it requires additional context to convey a clear meaning.
Example: "The alignments in the first section of the report need to be adjusted for better clarity."
Alternatives: "arrangements in the initial" or "positions in the first".
Since alignments can be ranked, correct assignments will be saved as unique alignments in the first filtering step (Figure S1).
This procedure will be repeated until all bund alignments in the first row have been determined.
The alignments in the first two classes were further processed using the Alpheus pipeline (Miller et al. 2008) for deriving per-gene read counts and sequence polymorphism calls.
The framework contains hand-curated reference phylogenies and alignments; in the first full release that we describe here (MLTreeMap version 2.011), these references encompass a total of 44 distinct gene families that have been selected to address both taxonomic as well as functional aspects of microbial assemblages.
Then the number of alignments in the second invocation with cost higher than the optimal one (as determined by the first invocation) is counted.
After 80 alignments in the fourth category were removed, each of the 299 remaining alignments was filtered to eliminate redundant or incomplete sequences (less than 50% of the average length of the alignment) using neighbor-joining (NJ) distance trees with bootstrapping (BP) using SeaView version 4.4.0 [ 60].
The example in Figure 1 shows such multiple alignments, in which the first sequence in each alignment indicates sequence A or B. Let Σ a and Σ b be the set of twenty distinct amino acids and one character representing a gap, and the set of four distinct bases and one gap character, respectively.
All analyses were also performed on "edited" alignments in which the first 40 45bp have been manually adjusted.
We analyzed all significant (E < 10−4) 'non-homologous' alignments found in the first three iterations of PSI-BLAST for the 100 queries (94 distinct families).
The final alignments used in the first approach consisted of 298 positions for the16S rDNA, 599 positions for COX1, 631 positions for 12S rDNA, and 709 positions for the 28S rDNA.
Holmes sustained the injury — to his Lisfranc ligament, a band of tissue that connects the front of his foot to the midfoot and is essential in maintaining the foot's alignment — in the fourth quarter of the Jets' 34-0 loss to San Francisco on Sunday.
