Modified pipeline for DNAWorks tool.

Clone this repo:

git clone https://github.com/lilpoundcake/Synt_v3.git

Go to the folder:

cd Synt_v3

First of all you need install xcode for macOS

xcode-select --install

You'll see a panel that asks you to install Xcode Command Line Tools. Click install. You'll see a confirmation message when installation is complete.

After that clone a repo with DNAWorks

git clone https://github.com/davidhoover/DNAWorks.git

Go to the directory with DNAWorks

cd DNAWorks

and edit output.f90 file:

bash
mv output.f90 output_old.f90 && \
sed -E "s/(12x\'  Tm Range = \',f4.1)/(12x,\'  Tm Range = \',f4.1)/g" output_old.f90 > output.f90

Compile:

make

If you receve an error when code is compiling

ld: warning: ignoring duplicate libraries: '-lemutls_w', '-lgcc'

ld: library 'System' not found

collect2: error: ld returned 1 exit status

make: *** [dnaworks] Error 1

use command:

export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"

and try to compile again:

make

Go back to upper level folder:

cd ..

In some cases there can be a problem with gfortran. So just use homebrew

brew install gcc

Install Gfortran:

apt-get install gfortran

After that clone a repo with DNAWorks

git clone https://github.com/davidhoover/DNAWorks.git

Go to the directory with DNAWorks

cd DNAWorks

Compile:

make

Go back to upper level folder:

cd ..

If you still don't have Miniconda or Micromamba - The time has come. Go to site and find appropriate information.

Install virtual environment with conda/micromamba:

conda env create -f env.yml

conda activate Synt_v3

For showing help enter:

python init.py -h

Tool supports several parameters:

• -n - name of project. Default name is synt_gene
• -p - protein or nucleotide. Default sequence type is protein
• -e - expression system. You may select one from list: cho, ecoli, sf9, human. Default is cho
• -t - preferable anneling temperature for PCR. Default temperature is 65 degrees Celsius.
• -l - by default primers will be designed with length less than 50 nt. You can choose another. Optimal value is between 50 and 60 nt. Integrated in the code module primer3 is not able to calculate thermadynamical properties for oligos longer then 60 nt.
• --tbio - thermodynamically balanced inside-out mode is 'True' by default
• --nogaps - there are gaps between oligos (mode is 'False' by default)

Let's try to design oligos:

python init.py -n My_Test_Project -p protein -e cho MAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLAD

You'll get new folder with your project name.

Folder contains files with generated sequences, primers lists, plots with heterodimer Tm, GC-content and so on.