When digesting DNA of an unknown plasmid (both single and double digestions with different enzymes), is there any software where I can give as input the fragment sizes and it solves the hypothetical restriction map?
Hi Rui,
Try NEBcutter. You past or upload your sequence of interest, select the type of enzyme then, you get the result.
Hope it helps.
http://nc2.neb.com/NEBcutter2/
The problem is that i don't have my sequence (yet). I just have "anonymous" fragments of different sizes and I want to try to put them in the estimated correct order (by comparison between diggestion with different enzymes and double diggestions).
NEB cutter works indeed fine. If you do a lot of plasmid construction, I can recommend "SerialCloner" to you. This is a program available as a free-ware and allows you to do virtual construction and mapping.
As mentioned the NEB cutter works well, but you need to enter the sequence, choose enzymes and then get a virtual map of the fragments. Webcutter, Restrictionmapper are other programmes for similar RE digest.
Rui, I am not sure if you have the plasmid sequence yet?
Hi Rui,
That is an interesting situation. Where did you get your plasmid? Do you need a precise map or just a general picture? I don't know of any software programs that will solve your restriction map but we used to give a (simple) version of this sort of question to students as an exam question. Essentially, it was a logic problem. If you can figure out the relative fragment sizes for single and double digestion fragments you can build up a possible map. However, tiny fragments (say 20 bp or less) wont' show up on your gel and bands of a similar size (within ~20%) will run together. Do you have any primer sets you could use to amplify and sequence regions of interest (especially any multiple cloning sites)? Best of luck!
Yes, Amy Klocko! It was basically an easier/faster way to solf that logic problem, to ger a general picture of my plasmid. Well, I guess I'll have to solve the puzzle the old fashion way.
Hi guys,
try Restriction Analyzer - free online tool for comprehensive restriction analysis of a DNA sequence.
http://www.molbiotools.com/restrictionanalyzer.html
- Badges
- Science topic