| ## RNAstructure Command Line Help oligoscreen and oligoscreen-smp | ### Contents ### Index
oligoscreen is used to calculate folding free energy changes for formation of unimolecular, bimolecular, and duplex structures for a set of oligonucleotides. The duplex folding is always fro the oligonucleotide (either RNA or DNA) binding to an RNA target. oligoscreen-smp is a parallel processing version for use on multi-core computers, built using OpenMP. ### USAGE: oligoscreen <list file> <report file> [options] ### OR: oligoscreen-smp <list file> <report file> [options] ### Required parameters:
<list file> | The name of a list file containing the oligos.
<report file> | The name of a report file to which output will be written. The report is tab-delimited and provides columns for the input sequence (Sequence), the bimolecular folding free energy change for two identical oligonucleotides interacting (DGbimolecular), the folding free energy change for unimolecular self-structure (DGunimolecular), the folding free energy change for duplex formation with the complementary sequence (DGduplex; where the complement is RNA), the cost of opening the two base pairs at the 5' end of the oligonucleotide in a duplex with the complementary sequence (DG2BPat5'), and the cost of opening the two base pairs at the 3' end of the oligonucleotide in a duplex with the complementary sequence (DG2BPat3'). Folding free energy changes are in kcal/mol.
### Options that do not require added values:
-d, -D, --DNA | Specify that the oligonucleotide sequences are DNA, and DNA parameters are to be used. (Note that the target is always RNA.) Default is to use RNA parameters.
-h, -H, --help | Display the usage details message.
### Options that require added values:
-t, -T, --temperature | Specify the temperature at which calculation takes place in Kelvin. Default is 310.15 K, which is 37 degrees C.
### Notes for smp: oligoscreen-smp, by default, will use all available compute cores for processing. The number of cores used can be controlled by setting the OMP_NUM_THREADS environment variable. ### References: Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). Matveeva, O.V., Mathews, D.H., Tsodikov, A.D., Shabalina, S.A., Gesteland, R.F., Atkins, J.F. and Freier, S.M. "Thermodynamic criteria for high hit rate antisense oligonucleotide design." Nucleic Acids Res., 31:4989-4994.(2003).