title: GeMS: an advanced software package for designing synthetic genes.
abstract: A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.
authors.affiliation: KOSAN Biosciences Inc. 3832 Bay Center Place, Hayward, CA 94545, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Jayaraj
authors.forename: Ralph
authors.initials: R
authors.lastname: Reid
authors.forename: Daniel V
authors.initials: DV
authors.lastname: Santi
mesh_terms: D001483:Base Sequence; D003062:Codon; D005813:Genes, Synthetic; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D016133:Polymerase Chain Reaction; D015183:Restriction Mapping; D012984:Software; D014584:User-Computer Interface
chemical_list: D003062:Codon; D009838:Oligodeoxyribonucleotides