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New (free) plasmid mapping program

plasmid map plasmid

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4 replies to this topic

#1 Bio-Lad

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Posted 13 June 2014 - 12:53 PM

Hey guys!  I wanted to give everyone a heads up about a new (and FREE) plasmid mapping/manipulation program that I've made.  I started a bit over a year ago making a tool for my own personal use here in lab and found it to be so useful that I decided to release it once I deemed it ready.  It's still a work in progress so if there are any glitches, I appreciate any info you may want to give.  It open Genbank format variants as well as the older pDRAW format (pDRAW has changed its format since I had programmed the file opening part but it will be updated soon).  Among other things you can:

  • Annotate new sequences from a library of known sequences (including degenerate DNA, degenerate amino acids, gapped, etc)
  • Adding, deleting, or modifying sequences in the library
  • Virtual gels for restriction enzymes (and mixes) you select
  • Searching sequences by DNA or amino acid sequence (again includes degenerate residues and gaps)
  • and more!

 

You can find information and the links to download on my blog (it's free, so I'm not paying my own money for a custom freakin' web site).

http://plasmidplotter.blogspot.com/

 

 

   -JM

pLOT+pX458.jpg


Edited by Bio-Lad, 13 June 2014 - 10:49 PM.

Try pLOT, the a free plasmid mapping tool!

http://plasmidplotter.blogspot.com/


#2 pito

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Posted 14 June 2014 - 03:20 AM

Can you already work with primers? (I read something on your website that primer mapping was not yet possible?)


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#3 Bio-Lad

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Posted 14 June 2014 - 07:18 AM

Not yet. You can still search for the primer sequences through the regular search. I do have the primer manager up so you can either manually enter primers or do a batch add. That way when the primer search is done (which will be really soon, probably a few days), you'll be ready.

Batch add can done simply by copying a table of primers from excel where the columns are:

Primer_name, sequence, comment, minimum anneal length (usually set to 15).

I did the batch add that way because we have a huge number of primers in our lab and it seemed a quick and convenient way to do it :-P

Try pLOT, the a free plasmid mapping tool!

http://plasmidplotter.blogspot.com/


#4 Bio-Lad

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Posted 22 June 2014 - 01:33 PM

Can you already work with primers? (I read something on your website that primer mapping was not yet possible?)

 

* Please note: v1.0.2 was replaced with 1.0.2b to reflect a quick fix to the search routine that would return the position of some results off by a single bp *

 

Just a heads up, the v1.0.2b update is now posted and allows the display of primers from your library as illustrated below biggrin.png

 

The download link for the update can be found at my blog: http://plasmidplotter.blogspot.com/

 

pUC19+Primers.jpg


Edited by Bio-Lad, 22 June 2014 - 01:33 PM.

Try pLOT, the a free plasmid mapping tool!

http://plasmidplotter.blogspot.com/


#5 Bio-Lad

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Posted 23 June 2014 - 05:03 AM

I've heard that there was a problem with some people using the 1.0.2b update and getting an error with a missing .dll.  If that happened, uninstall the old version and re-install from the 1.0.2b complete install file (in the newest post and updated in the previous one.).


Try pLOT, the a free plasmid mapping tool!

http://plasmidplotter.blogspot.com/






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