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The G-patch is a glycine-rich domain discovered by sequence alignment, involved in protein-protein and protein-nucleic acid interaction.
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Alignment issues involved in ribosomal RNA data were addressed by an array of measures proven to be beneficial ([ 20]; see Section 2).
If linguistic alignment involves normalisation in the statistical sense described here, then the positive effect of linguistic alignment could depend on the similarity of dyad members' reliabilities.
Being alignment-free renders the method parameter-free, as sequence alignment involves many parameters embodied in the elements of scoring matrices and gap penalties.
Consider, for example, the alignment shown in Figure 2. The first segment in this alignment involves a noticeable amplitude difference (Time Series B has a higher amplitude than Time Series A), and the last segment involves significant stretching (this part of the response in Time Series B happens more slowly than the corresponding part of Time Series A).
Hence, any substitution in the alignment involving a synonymous or noncoding site was determined to either involve a CpG dinucleotide or not.
Alignment sections presumably involved in the formation of pseudoknots were locked from folding to avoid artifacts.
This fine scale alignment involves a local warping of each embryo described in detail previously (Fowlkes et al., 2008).
TW participated in project conception, preparation of figures, did sequence alignments and was involved in manuscript drafting.
SLS helped conceive of the study, participated in its design, carried out sequence alignments and was involved in interpretation of the results and drafting of the manuscript.
The first stage of MUMmer alignment involves identifying alignment anchors.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com