Example for requesting evaluation of secondary structure prediction accuracy

Bold face: keyword "evaluate prediction accuracy"

NOTE: input MUST be in column format and MUST contain prediction and experimental assignment.
Effect: scores for per-residue and per-segment accuracy are returned

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu 
joe@amino.churn.edu
evaluate prediction accuracy
# COLUMN format , incredulase from paracoccus dementiae, translated from cDNA
NAME     AA  PSEC OSEC
first    M   L    L
first    Q   L    L
first    T   L    H
first    S   H    H
first    E   H    H
first    R   H    H
first    L   H    H
first    A   L    H
first    G   L    L
first    V   L    L
first    K   L    L
first    Q   H    H
first    Q   H    H
first    S   H    H
first    I   H    H
second   G   L    L
second   V   L    L
second   K   E    L
second   Q   E    H
second   Q   E    H
second   S   L    H
second   I   L    H

Compulsory information: (1) predicted secondary structure (PSEC) in either of the states H=helix, E=strand, or L=rest; (2) observed secondary structure (OSEC) in either of the states H=helix, E=strand, or L=rest (e.g. from DSSP assignment); (3) if more than one protein is used, simply append all requested proteins (in that case make sure that the first column (NAME) lists a unique protein name).

Optional: (1) sequence (AA) in one-letter code; (2) name of protein (compulsory for more than one protein).