DNA Software uses special file formats for input, output, numerical analysis and structure. Common file formats such as Fasta and Genbank are unable to encapsulate all of the information needed to run a simulation thus necessitating these unique file formats. All file formats are compatible boulder I/O text file formats for ease of customizability and scripting.
OMP Design File (ODF)
Contains all of the information necessary to design single or multiplex primers and/or probes given at least one starting target sequence. Contains information about sequences, solution conditions, output constraints, weights, directory information, and possible amplicon information. An ODF may contain a design for a probe, a TaqMan probe, an allele probe pair, a primer pair, a reverse primer, a forward primer, a fixed probe, an RNA probe, a beacon probe or a beacon probe pair.
OMP Experiment File (OEF)
Contains all of the information necessary to run an experimental simulation. Contains information about sequences, solution conditions, output constraints, weights, directory information, and Net TM.
OMP Output File (OOF)
Contains the results of a simulation (OEF). The OOF contains species specific thermodynamics, extensible information as well as concentration and percent bound values that are generated by Visual OMP. Both the results summary and the crosshybridization grid are generated from the OOF.
OMP Output File (OSF)
Contains the results of a design (ODF). The OSF contains the designs and thermodynamics associated with single or multiplex probe and primer design.
Numerical Analysis File (NAL)
Contains all results of
a simulation for a numerical analysis. I
.e. the concentrations of all species at temperatures from 10 to 100
Traceback Structure File (TBS)
Each TBS file contains base pairing information about a single species which is used by Visual OMP to draw a graphical representation.
Scorpion Input File (SIF)
Contains all of the information necessary to run a scorpion design. Contains information about sequences, solution conditions, output constraints, weights and directory information.
Scorpion Output File (SOF)
Contains the results of a scorpion design (SIF). The SOF contains the designs and thermodynamics associated with the designed scorpions.