Sentence examples for for the effect of alignment from inspiring English sources

Second, one can rather easily estimate an upper bound for the effect of alignment bias by randomly permuting the sequences, realigning them, and performing the model selection tests with PhyML [ 119] or MrBayes.

For estimating the effect of alignment shifts in models with otherwise correct fold and stereochemistry, we created pseudomodels starting from the original protein structure and introducing threading errors of increasing magnitude for different representative structure architectures from CATH (Cuff et al., 2011).

The duplicated nodes were assigned the same sequences of their original nodes respectively, to avoid the effect of alignment for non-duplicated nodes as much as possible.

The effect of alignment bias is maximal for random sequences where it results in a highly uncertain alignment with spurious similarities; it is minimal for sequences of high similarity where the alignment is relatively certain; and the bias vanishes in the limiting case of long identical sequences where no alignment uncertainty exists.

Figure  5 demonstrates the effect of alignment in the case of using 2-nonanone for alignment of an analysis of the 15-analyte mixture (see Table  1).

Quantitative assays are needed to determine the effect of alignment on contractile function and muscle physiology.

To isolate the effect of alignment we applied a linear SVM to the alignment model determined by the HMM.

As previously suggested, our results underscore the importance for careful exploration of the sensitivity to the effects of alignment methods for data comprising widely divergent sequences.

The effects of alignment size bias are especially noticeable for alignments containing fewer than about 100 sequences, and must be accounted for when making direct comparisons between sequence alignments of different sizes.

The concordance rates were generally lower for variant call sets based on the Bowtie 2 with respect to BWA, alignments, which can be partly explained by the relatively higher accuracy of variant calls based on BWA alignments (for the effect of the aligners on variant calling, see Additional file 1: Supplementary results).

controls for the effects of different alignment algorithm (BLAST versus Smith Waterman) and similarity thresholds compared to CluSTr.