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A notable difference among solved sHSP ACD structures is that dimers appear in different alignments of the two β6+7 strands (Clark et al., 2011; Hochberg et al., 2014).
Theoretically, single copy genes with highly divergent alleles could end up in separate clusters, and therefore in different alignments (or as singleton sequences), due to their high number of nucleotide differences.
Identifying ab initio conserved regions in different alignments and combining them in a single consensus alignment is more complicated.
However, more generally, an essential part of the SIFT procedure is to find homolog sequences in a database like UniProt/TrEMBL via PSI-BLAST, which naturally results in different alignments and different sets of scorable mutations.
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Importantly, the method used here does not require multiple sets of RDC data acquired in different alignment media.
Since knee alignment have great impact on biomechanical force transmission which may influence the degree of extrusion, a larger sample allowing enough numbers in different alignment categories would be valuable in future work [ 34].
Both of the latter two cases had multiple best hits but resulted in different alignment choices probably due to insert size statistics, in turn due to the particular input read batch.
The stringency settings for adoption of secondary structures in different alignment steps was relaxed (0.51), as we wanted to retain as much structure information as possible (see [ 30] for a detailed description of the RNA SALSA method).
Additional properties such as the number of gaps and number of constant sites in the different alignments are shown in Table 2. Estimates of potential sequencing errors in Sminthopsis ESTs indicated an error rate of approximately 0.01% and allelic variation of about 0.02%.
Polyester yarn with the tenacity of 31.77 cN/tex was pooled with 2.70 cN/tex copper wire in two different alignments (Figs. 1, 2).
# of variable sites: positions that constitute more than one amino acid in the different alignments.
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