title: Gene composer: database software for protein construct design, codon engineering, and gene synthesis.
abstract: BACKGROUND
  To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering.
  
  
  RESULTS
  An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies.
  
  
  CONCLUSIONS
  We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.
authors.affiliation: deCODE biostructures, Inc 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. dlorimer@decode.com
authors.forename: Don
authors.initials: D
authors.lastname: Lorimer
authors.forename: Amy
authors.initials: A
authors.lastname: Raymond
authors.forename: John
authors.initials: J
authors.lastname: Walchli
authors.forename: Mark
authors.initials: M
authors.lastname: Mixon
authors.forename: Adrienne
authors.initials: A
authors.lastname: Barrow
authors.forename: Ellen
authors.initials: E
authors.lastname: Wallace
authors.forename: Rena
authors.initials: R
authors.lastname: Grice
authors.forename: Alex
authors.initials: A
authors.lastname: Burgin
authors.forename: Lance
authors.initials: L
authors.lastname: Stewart
mesh_terms: D000465:Algorithms; D003001:Cloning, Molecular; D003062:Codon; D019295:Computational Biology; D030541:Databases, Genetic; D005813:Genes, Synthetic; D015202:Protein Engineering / Q000379:methods*; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D003062:Codon