title: BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.
abstract: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment.
  
  
  
  BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder
  
  
  
  joel.bader@jhu.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.
authors.forename: Kun
authors.initials: K
authors.lastname: Yang
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Stracquadanio
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA.
authors.forename: Jingchuan
authors.initials: J
authors.lastname: Luo
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA.
authors.forename: Jef D
authors.initials: JD
authors.lastname: Boeke
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.
authors.forename: Joel S
authors.initials: JS
authors.lastname: Bader
mesh_terms: D004247:DNA; D011381:Programming Languages; D058615:Synthetic Biology
chemical_list: D004247:DNA