|
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]
| <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. |
| -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. |
| -t, -T, --temperature |
Specify the temperature at which calculation takes place in Kelvin.
Default is 310.15 K, which is 37 degrees C.
|
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.
-
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).
|
