.TH "compstruct" 1 "January 2003" "Biosquid 1.9g" "Biosquid Manual"

.SH NAME
.TP 
compstruct - calculate accuracy of RNA secondary structure predictions

.SH SYNOPSIS
.B compstruct
.I [options]
.I trusted_file
.I test_file

.SH DESCRIPTION

.I compstruct 
evaluates the accuracy of RNA secondary structure predictions, at the
on a per-base-pair basis.
The 
.I trusted_file 
contains one or more sequences with trusted (known) RNA
secondary structure annotation. The
.I test_file
contains the same sequences, in the same order, with
predicted RNA secondary structure annotation.
.I compstruct 
reads the 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 together.

.PP
Both files must contain secondary structure annotation in
WUSS notation. Only SELEX and Stockholm formats support 
structure markup at present.

.PP
The default definition of a correctly predicted base pair
is that a true pair (i,j) must exactly match a predicted
pair (i,j).

.PP

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
.B -m
option 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).


.SH OPTIONS

.TP
.B -h
Print brief help; includes version number and summary of
all options, including expert options.

.TP
.B -m
Use the Mathews relaxed accuracy rule (see above), instead
of requiring exact prediction of base pairs.


.TP
.B -p 
Count pseudoknotted base pairs towards the accuracy, in either trusted
or predicted structures. By default, pseudoknots are ignored. 
.IP
Normally, only the 
.I trusted_file 
would have pseudoknot annotation, since most RNA secondary structure
prediction programs do not predict pseudoknots. Using the
.B -p
option allows you to penalize the prediction program for not
predicting known pseudoknots. In a case where both the
.I trusted_file 
and the
.I test_file 
have pseudoknot annotation,  the
.B -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
.I test_file,
but the 
.I trusted_file 
does not have pseudoknot annotation; in this case,
.B -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.

.SH EXPERT OPTIONS

.TP
.BI --informat " <s>"
Specify that the two sequence files are in format 
.I <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).

.TP
.B --quiet
Don't print any verbose header information.


.SH SEE ALSO

.BR afetch (1),
.BR alistat (1),
.BR compalign (1),
.BR revcomp (1),
.BR seqsplit (1),
.BR seqstat (1),
.BR sfetch (1),
.BR shuffle (1),
.BR sindex (1),
.BR sreformat (1),
.BR stranslate (1),
.BR weight (1).

.SH AUTHOR

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 contact me.

.nf
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX  : 1-314-362-2157
Email: eddy@genetics.wustl.edu
.fi