compstruct(1)							  Biosquid Manual						     compstruct(1)

NAME

       compstruct - calculate accuracy of RNA secondary structure predictions

SYNOPSIS

       compstruct [options] trusted_file test_file

DESCRIPTION

       compstruct  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 test_file contains the same sequences, in  the  same  order,
       with  predicted RNA secondary structure annotation.  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.

       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 option activates this rule for both  sensitivity  and  for  speci-
       ficity. 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).

OPTIONS

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

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

       -p     Count pseudoknotted base pairs towards the accuracy, in either trusted or predicted structures. By default, pseudoknots are ignored.

	      Normally, only the trusted_file would have pseudoknot annotation, since most RNA secondary structure prediction programs do not pre-
	      dict  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  calcu-
	      lates  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.

EXPERT OPTIONS

       --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).

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

SEE ALSO

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

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.

       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

Biosquid 1.9g							   January 2003 						     compstruct(1)