PlasmaDNA

PlasmaDNA is a small software application developed specifically for helping you analyze and manipulate DNA sequences. It can be deployed on all Windows versions out there.

Portable tool

This is a portable tool. You can store it on USB flash drives or other portable devices to have it with you all the time. In addition, you may run it without administrative privileges.
Gaining access to its features requires only opening the executable file because there’s no setup included in the process. It does not write entries to your Windows registry and leave other configuration files on the target PC. It actually saves the settings data on the storage device. Getting rid of it implies a simple deletion task of the files that you have downloaded from the Internet.

User interface

You are welcomed by a clean workspace where you can hide or show several analysis tools. A help manual is included in the package in case you need to know more about the application’s features.

DNA manipulation features

PlasmaDNA comes with support for an automatic analysis mode of DNA sequences for restriction sites, primer binding sites, as well as common plasmid domains.
Plus, the tool is capable of keeping track of multiple sequences at the same time. It lets you work with several analysis methods that deal with in silico digestion with restriction enzymes, in silico polymerase chain reaction (PCR), and in silico Gateway recombination between compatible fragments.
What’s more, you are allowed to perform an automatic determination of cloning strategies and import/export multiple sequences with FASTA file format.
PlasmaDNA lets you clear the current session (by deleting all fragments) from the worskspace, show/hide the overlay of percent GC-content of the DNA fragment, enter custom comments in a dedicated panel, and use all the enzymes present in the enzyme database or those present in your laboratory.
You can add new fragments (by copying/pasting/importing data), visually analyze the fragments, perform PCR or ligate compatible fragments, invert DNA fragment, rotate the fragment, set the name of the fragment, digest the current fragment with a restriction enzyme, add a new primer to the PlasmaDNA database, circularize the current fragment, and get a summary of all the restriction sites, domains, primers, open reading frames, and primary DNA sequence of the fragment.
Other notable features worth being mentioned enable you to perform an automatic cloning of a fragment from one plasmid to another, save fragments to a PlasmaDNA file format (POF), export the selected sequences to FASTA files, and save the graphical view of one fragment to JPEG images.

Final observations

To sum things up, PlasmaDNA proves to be a reliable and comprehensive DNA analysis and manipulation application that comprises smart tools for designing cloning strategies, generating sequences of new clones, and archiving cloning strategies.