Table 1.

Stand-alone tools available in the GeMS software package

GeMS software tool	Function
DNA–protein
Translation	Translates a DNA sequence into a protein sequence
Reverse complement	Reports the reverse complement of a DNA sequence
Sequence alignment	Aligns protein or DNA sequences based on local similarities
DNA stem–loops	Reports inverted repeats in a DNA sequence
Assign vectors for LBS	Assigns vectors to synthons for ligation-by-selection
Restriction sites
Restriction sites in DNA	Reports restriction sites in a DNA sequence
Predict all possible sites from protein	Reports all possible restriction sites
Automatic spacing of unique sites	Spaces unique sites over a designed gene sequence
Exclude sites	Excludes restriction sites while preserving protein sequence
Codon usage
Custom codon table	Creates a custom codon preference table
Hybrid codon table	Creates a custom codon preference table for multiple organisms
Codon optimize	Optimizes codons in a DNA sequence for a desired organism
Oligo design
Tm	Calculates melting temperature of complementary DNA sequences
Design 40mers	Designs 40mer oligo components of a DNA sequence
Design 40mers + primers	Designs 40mer oligo components of a DNA sequence with primers