compstruct [options] trusted_file test_file
- compstruct - calculate accuracy of RNA secondary structure
evaluates the accuracy of RNA secondary structure predictions,
at the on a per-base-pair basis. The trusted_file
contains one or more
sequences with trusted (known) RNA secondary structure annotation. The
contains the same sequences, in the same order, with
predicted RNA secondary structure annotation. compstruct
structures and compares them, and calculates both the sensitivity (the number
of true base pairs that are correctly predicted) and the specificity (positive
predictive value, the number of predicted base pairs that are true). Results
are reported for each individual sequence, and in summary for all sequences
Both files must contain secondary structure annotation in WUSS notation. Only
SELEX and Stockholm formats support structure markup at present.
The default definition of a correctly predicted base pair is that a true pair
(i,j) must exactly match a predicted pair (i,j).
Mathews, Zuker, Turner and colleagues (see: Mathews et al., JMB 288:911-940,
1999) use a more relaxed definition. Mathews defines "correct" as
follows: a true pair (i,j) is correctly predicted if any of the following
pairs are predicted: (i,j), (i+1,j), (i-1,j), (i,j+1), or (i,j-1). This rule
allows for "slipped helices" off by one base. The -m
activates this rule for both sensitivity and for specificity. For specificity,
the rule is reversed: predicted pair (i,j) is considered to be true if the
true structure contains one of the five pairs (i,j), (i+1,j), (i-1,j),
(i,j+1), or (i,j-1).
- Print brief help; includes version number and summary of
all options, including expert options.
- Use the Mathews relaxed accuracy rule (see above), instead
of requiring exact prediction of base pairs.
- Count pseudoknotted base pairs towards the accuracy, in
either trusted or predicted structures. By default, pseudoknots are
- Normally, only the trusted_file would have
pseudoknot annotation, since most RNA secondary structure prediction
programs do not predict pseudoknots. Using the -p option allows you
to penalize the prediction program for not predicting known pseudoknots.
In a case where both the trusted_file and the test_file have
pseudoknot annotation, the -p option lets you count pseudoknots in
evaluating the prediction accuracy. Beware, however, the case where you
use a pseudoknot-capable prediction program to generate the
test_file, but the trusted_file does not have pseudoknot
annotation; in this case, -p will penalize any predicted
pseudoknots when it calculates specificity, even if they're right, because
they don't appear in the trusted annotation; this is probably not what
you'd want to do.
- --informat <s>
- Specify that the two sequence files are in format
<s>. In this case, both files must be in the same format. The
default is to autodetect the file formats, in which case they could be
different (one SELEX, one Stockholm).
- Don't print any verbose header information.
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington
University School of Medicine Freely distributed under the GNU General Public
License (GPL) See COPYING in the source code distribution for more details, or
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
FAX : 1-314-362-2157