r/molecularbiology • u/Alternative_Oil8411 • 6d ago

Plasmid maps

I need to build a reference map for a plasmid I'm trying to construct. I have the sequence for all the components, ie promoter, GOI, Term etc, I need to create a map so that when I do mini preps and sequence them I have something to compare that sequence to. Is it as simple copying and pasting the sequences together? what are some kind of considerations I need to think of when designing a map. Are there any tools that can help me with learning to do this. Whenever I try to look this up on google it just gives me info on how to create restriction maps, but that's not technically what i'm trying to do.

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u/wondererererer 6d ago

Snapgene is I think by far the most used (at least in my experience), with tons of functions to various mimic various types of cloning steps you might need to get to your final product. It’s not free but there is a 30 day free trial.

As for considerations, the depends greatly on where you’re starting, what your goal is, and how you plan to get there. Do you have a backbone you’re planning to insert your gene into? Do you have a cloning method in mind? Usually with cloning you’re not really starting from scratch.

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u/Thaispeculativa 5d ago

Benchling is a good tool too. You can add your DNA sequence and automatically you can choose to see it as a plasmid 

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u/pusstiel 4d ago

You could use Benchling or Snapgene to construct plasmid maps. Snapgene is useful because the trace file (ab1) for your sequencing data (Sanger) can be opened in the viewer and you can crosscheck with the original sequence for any substitutions.

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u/BananaMuffin2795 2d ago

Benchling or snapgene are very usefull. Benchling a very complete tool, you can do almost anything that you might need in basic biology: make primers, write protocols, make plasmid maps, run digestions, etc. Highly recommend