Valentin Zulkower1, Susan Rosser1. 1. Edinburgh Genome Foundry, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh EH93BF, UK.
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.
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.
Authors: Josh Tycko; Nicole DelRosso; Gaelen T Hess; Abhimanyu Banerjee; Aditya Mukund; Mike V Van; Braeden K Ego; David Yao; Kaitlyn Spees; Peter Suzuki; Georgi K Marinov; Anshul Kundaje; Michael C Bassik; Lacramioara Bintu Journal: Cell Date: 2020-12-15 Impact factor: 66.850
Authors: Meghan E Garrett; Jared Galloway; Helen Y Chu; Hannah L Itell; Caitlin I Stoddard; Caitlin R Wolf; Jennifer K Logue; Dylan McDonald; Frederick A Matsen; Julie Overbaugh Journal: bioRxiv Date: 2020-11-16