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oligoscreen

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oligoscreen is used to calculate thermodynamic parameters for a group of oligonucleotides.

USAGE: oligoscreen <list file> <report file> [options]

Required parameters:

<ct file>	The name of a file containing the oligo list.
<report file>	The name of a report file to which output will be written.

Options which don't require added values:

-d, -D, --DNA	Specify that the sequence is DNA, and DNA parameters are to be used. Default is to use RNA parameters.
-h, -H, --help	Display the usage details message.

Options which 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.

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)

RNAstructure Help oligoscreen