SEQMAK (pronounced SEC-mac) is a program for producing DNA sequences. Much of the inspiration for SEQMAK comes from SEQUIN which was written by Ned Seeman (1, 2). The main differences are

• much of the repetitive nature of SEQUIN has been automated with some added functionality (e.g. dyad symmetry checking),

• exception handling has been much improved, and

• all features have been modularized, making the code much easier to read, learn, and maintain.

As is the case with SEQUIN, kinetic and thermodynamic factors are not taken into account when designing structures with SEQMAK . Only different combinations of DNA bases are considered. If you would like to consider other factors when designing your DNA structure, you may want to use a more complex program such as DNAdesign.

SEQMAK is written in Python 2.7. In order to run the program you must have Python installed on your computer (preferably version 2.7x but version 2.4x should also work). This software has not been tested with Python 3.0 or higher, so I cannot guarantee it will work under those environments. If you do not have Python installed on your computer, you may download the latest version at http://www.python.org/download/.

All python package dependencies can be installed using pip. pip does not come pre-installed with the python virtual machine, so you need to install it manually.

• Install pip (if you do not have it installed)

# yum install python-pip

or

$ sudo apt-get install python-pip

for GNU/linux machines.

• Upgrade pip.

$ sudo pip install pip --upgrade

• Install all required dependencies by typing

$ pip install -r requirements.txt

Read the Introduction of the manual for information on running the program.

If you use this software, please cite it as:

"N. C. Seeman and N. R. Kallenbach, "Design of immobile Nucleic Acid Junctions", Biophysical Journal 44, 201-209 (1983)"

"N. C. Seeman, "De Novo Design of Sequences for Nucleic Acid Structural Engineering", Journal of Biomolecular Structure & Dynamics 8, 573-581 (1990)"