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 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).
afetch(1), alistat(1), compalign(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1).
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: firstname.lastname@example.org