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Sequences were edited using the BioEdit Sequence Alignment Editor version 7.0.5.3 [21].
The sequences were aligned using the BioEdit Sequence Alignment Editor (Tom Hall, Ibis Therapeutics).
Sequences were compared to those of the wild-type genes of strain H37Rv (http://www.ncbi.nlm.nih.gov) using the BioEdit Sequence Alignment Editor.
Sequencing results were analyzed using the BioEdit sequence alignment editor (Ibis Biosciences); primer sequences were removed and nucleotide similarity comparisons were made using the GenBank database.
Initial sequence alignment was performed using the software MUSCLE available online (http://www.ebi.ac.uk/Tools/muscle/index.html) [50], [51], and subsequently optimized by eye using the Bioedit Sequence Alignment Editor v5.09 [52].
Sequences were assembled and aligned by using the BioEdit Sequence Alignment Editor software [ 53].
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The AprBA sequences were implemented into the persisting multiple alignment of SRP- and SOB-derived sequences [16], [17] using the Bioedit (version 7.0.5) sequence alignment editor (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
Sequence alignments for the selection of PCR target regions were generated using the BioEdit 7.0.9 software after sequence download from NCBI National Center for Biotechnology Informationn, http://www.ncbi.nlm.nih.gov).nih.gov
We then aligned and unified the sequences with the clustalW program using the BioEdit software to unify the sequences from different labs that used different primers.
Primer sequences were removed from all sequences using the BioEdit program (version 7.0.5.3) [ 58].
Sequences were trimmed, concatenated and aligned with all published sequences using the BioEdit 7.2.2 software [ 16].
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