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The gap was replaced by the scene of River flying the TARDIS after the Byzantium, which was filmed as a pick-up.
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A window around each artifact is removed and the entire filtered, cleaned dataset is fit with a spline such that clean peaks are modeled and the windowed gaps are replaced with values from the spline interpolation to produce a clean, spline waveform (Figure 2).
Heuristic "costs" for opening and extending gaps are replaced by the insertion/deletion rate and the mean indel length respectively, which are biologically interpretable parameters and can be estimated from the data without circularity [ 22, 23].
In case an alignment A' in A contains some gaps, each sequence S in A' that contains gaps is replaced by the set of all sequences obtained by replacing the gaps in S with all possible nucleotide symbol combinations (or the set of nucleotides actually observed at the gap containing position).
The GAP promoter was replaced with AOX1 cut from pPICZA (Invitrogen) with a BglII/BstBI digest.
Insertions-deletions ("indels") were coded like SNPs: each gap, irrespective of its length, was replaced by a nucleotide producing a SNP to treat indels in subsequent analyses.
In addition to analysing each gene separately, a concatenated alignment of the six mitochondrial genes was generated, and if any taxon was missing a gene it was replaced by gaps.
The original Gap logo, showing the word "Gap" in capital letters inside a dark blue square, was replaced with a white square encasing a small blue square sitting over the letter "p" in "Gap".
In Gap 4, a 1140-bp sequence in A. flavus was replaced by unrelated 6138-bp sequence in A. sojae (Fig. 7A).
In Gap 7, a 2761-bp sequence in A. flavus was replaced by unrelated 11 493-bp sequence in A. sojae (Fig. 7B).
First, the URA3 marker was replaced with a LEU2 marker by gap repair using the AatII/ PvuII LEU2 fragment of pRS305.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com