Repp

Biologists profit when they can re-use DNA during plasmid design: it enables cheaper designs and faster builds. But parsing through all re-usable DNA is completely infeasible. For example, there are over 75,000 plasmids in Addgene -- the likelihood of knowing the best combination and ordering of sub-sequences from Addgene for a given plasmid design is low.

Repp is made to enable such plasmid design. It turns arbitrary plasmid sequences into designs using the least expensive design with both existing DNA fragments (PCR) and newly synthesized DNA fragments. Repp was written to minimize plasmid design costs and simply the design process.

Installation

Download links are available at SourceForge: https://sourceforge.net/projects/repp/files/

MacOS/Linux

wget -O repp_src_0.1.0.tar.gz 'https://sourceforge.net/projects/repp/files/repp_src_0.1.0.tar.gz/download'
tar xzf repp_src_0.1.0.tar.gz
cd repp_src_0.1.0
make install

Windows

1. Download the most recent repp_windows.*.zip file
2. Unzip
3. Run repp_install.exe

Design

See repp --help and the application documentation for more depth and examples.

Sequence-based design

To design a plasmid sequence in a local FASTA file called desired_plasmid.fa using Addgene and a local parts database parts_library.fa:

repp make seq -in ./desired_plasmid.fa --addgene --dbs parts_library.fa

To construct a plasmid in desired_plasmid.fa, with less consideration for sequence exactness and using all sequences in Addgene, DNASU, and iGEM:

repp make seq -in ./desired_plasmid.fa --addgene --dnasu --igem --identity 94