|
CircleCompare is used to compare two nucleic acid structures for the same sequence by
arranging them on top of one another around a circle. This layout
makes base pairs and pseudoknotted pairs easily visible.
USAGE: CircleCompare <predicted ct> <accepted ct>
<ps file> [options]
| <predicted ct> |
The name of a file containing CT data for the predicted
structure.
|
| <accepted ct> |
The name of a file containing CT data for the accepted
structure.
|
| <ps file> |
The name of a Postscript image file to which output will be
written.
|
| -a, -A, --alternative |
Specify that an alternative color scheme should be used.
CircleCompare uses the following color scheme when
identifying secondary structure pairs:
| Green |
Present in predicted and accepted structures |
| Red |
Present in predicted structure only |
| Black |
Present in accepted structure only |
The alternative color scheme is similar to the default, but
the colors used for accepted and predicted pairs differ:
| Green |
Present in predicted and accepted structures |
| Purple |
Present in predicted structure only |
| Red |
Present in accepted structure only |
|
| -e, -E, --exact |
Specify exact comparison when structure comparison is scored.
When exact comparison is specified, a known base pair between
nucleotides i and j is considered to be
correctly predicted only by the base pair i-j.
By contrast, when flexible pairings are allowed, base pairs are considered to be correctly
predicted when one of the two indices is different by up to one nucleotide. This better accounts for RNA dynamics and uncertainty in the RNA structure. For a known base pair i-j, all of
the following predicted pairs are considered correct with
flexible pairings:
- i — j
- i — j-1
- i — j+1
- i-1 — j
- i+1 — j
Default is to allow flexible pairings.
|
| -f, -F, --firstOnly |
Specify that only the first structure in the predicted ct
file should be compared with the accepted structure.
Default is that all structures in the predicted ct file are
compared with the accepted structure.
|
| -h, -H, --help |
Display the usage details message. |
| -p, -P, --probability |
Specify the name of the file from which base pairing
probability data will be read for annotation. This file must
be a partition function save file.
Default is no probability annotation file used.
|
| -s, -S, --SHAPE |
Specify the name of the file from which SHAPE data will be
read for annotation.
This annotation is not structure dependent.
Default is no SHAPE annotation file used.
|
-
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
-
Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H.
"Expanded sequence dependence of thermodynamic parameters
provides improved prediction of RNA secondary structure."
J. Mol. Biol., 288:911-940. (1999).
|
|
