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After adapter removal and low-quality trimming, any sequences shorter than 50 bp were removed from each data set.
Sequences with more than 1 mismatch to the barcode, two mismatches to the primer or homopolymers >8 bp were removed from the dataset.
For motAB, 658 bp were removed from the middle to the end of the motA gene, leaving the first 52 amino acids of motA intact, and resulting in a deletion of 83% of motA.
To determine whether the putative cryptic promoter elements were functioning in E. coli, 50, 67 or 85 bp were removed from the 5' end of the DENV2 cDNA in pD2-GFP to produce the plasmids pΔ50D2-GFP, pΔ67D2-GFP and pΔ85D2-GFP, respectively.
Additionally, reads shorter than 100 bp were removed from consideration.
After cleaning, sequences ≤30 bp were removed from the dataset.
Similar(42)
The construct designated V5PB pDNA (6.4 kbp) was made as follows: the 3′UTR fragment of the Xenopus laevis β-globin gene (designated U3, 317 bp) was removed from pBSSK/SB10 (kindly supplied by Dr.Z. Ivics, Max Delbrück Center, Germany), and inserted into pCS2+ already containing the 5′UTR (designated U5) (Invitrogen/Life Technologies, Paisley, UK).
A Perl program was written to remove vector sequences and the PolyA (T) tail from sequences; reads with lengths <100 bp were removed before assembly.
Reads shorter than 200 bp were removed.
Briefly, ESTs <300 bp were removed, along with chloroplast, mitochondrial or rDNA ESTs.
(2) Reads failed matching the PHRED score (<0.01) and length (≥40 bp) were removed.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com