DNA Chisel, a versatile sequence optimizer

Abstract

Motivation: Accounting for biological and practical requirements in DNA sequence design often results in challenging optimization problems. Current software solutions are problem-specific and hard to combine.

Results: DNA Chisel is an easy-to-use, easy-to-extend sequence optimization framework allowing to freely define and combine optimization specifications via Python scripts or Genbank annotations.

Availability and implementation: The framework is available as a web application (https://cuba.genomefoundry.org/sculpt_a_sequence) or open-source Python library (see at https://github.com/Edinburgh-Genome-Foundry/DNAChisel for code and documentation).

Supplementary information: Supplementary data are available at Bioinformatics online.