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We aligned the genome dataset using the program MUSCLE [18] to produce an alignment that was 16017 nucleotides long.
Removal of the hypervariable regions resulted in an alignment that was significantly more structured than random data, as indicated by the measure of skewness (Table 2).
The 104 alignments were then concatenated, leading to an alignment that was 39,926 residues long.
Sequences were aligned using MUSCLE v3.8.31; the relatively small number of apparent insertion/deletion events led to an alignment that was <0.3% gap.
Similar(55)
Instead, AR attempts to provide an alignment that is very close with little difference in terms of the shape Tanimoto and graphical display.
It traveled east to Fennville then turned south to Pearl before turning back to the east towards Allegan on an alignment that is a few miles south of the present day configuration.
These tRNAs have cloverleaf secondary structures that were derived by comparative analysis using an alignment that is most compatible with tRNA phylogenies and known 3-dimensional models of structure [91], [92].
Conversely, an alignment that is robust to reversing the sequences supports the original alignment.
In this contribution, we present a new method for determining "noisy" sites in an alignment that is not a priori restricted to tree-like data.
Importantly, this implies that for the real network data set it might be hard to produce an alignment that is of excellent quality both topologically and biologically.
To correct these conservative annotations, we compared the bare domain query sequences to the target library using SSEARCH and GLSEARCH (a program that produces an alignment that is global in the query sequence but possibly local in the target or library sequence).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com