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E.coli strains that have dam or dcm methylases can methylate plasmid at adenines or cytosines respectively. See here — It is a NEB web page but has links to the cited references. DH5α has both the methylases- dam+ dcm+ , BL21 is dam+ dcm− and ET12567 is dam− dcm−


For protein alignment you have things like Clustal W/Clustal X. Many, including myself use R for bioinformatics related work and I have came across this package which can be found in Bioconductor, which can address one of your points but I don't know of any unified CLI for the points you have said. I haven't worked with that specific package itself but if ...


Making maps of plasmids Annotating plasmids with common features Plasmapper works through commandline Finding restriction sites Simple regex searches can do that Mapping Sanger sequencing reads BLAST will do it. Showing sequence, reverse complement of the sequence, translations in different frames EMBOSS has a collection of tools ...

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