Secondary structure prediction is notoriously difficult to do accurately. The GOR I alogorithm is one of the first semi-successful methods.
The Garnier method is not regarded as the most accurate prediction, but is simple to calculate on most workstations.
The accuracy of any secondary structure prediction program is not much better than 70% to 80% at best. This is an early algorithm and will probably not predict with much better than about 65% accuracy.
The Web servers for PHD, DSC, and others are generally preferred.
Do not rely on this (or any other) program alone to make your predictions with. Use several programs and take a consensus of the results.
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The meaning and use of the parameter 'idc' is currently being investigated. The original author, Bill Pearson writes:
"In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. "idc" is an index into a set of arrays, dharr[] and dsarr[], which provide "decision constants" (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used. I don't remember what they are, but I must have gotten the values from their paper."
By default garnier writes a 'tagseq' report file.
The Web servers for PHD, DSC, and others are generally preferred.
Do not rely on this (or any other) program alone to make your predictions with. Use several programs and take a consensus of the results.
The 3D structure for the example sequence is known, although the 2D structure elements were not in the SwissProt feature table for release 38 when the test data was extracted.
DSSP shows:
 From     To   Structure
    9     13   E beta sheet
   21     39   H alpha helix
   50     54   E beta sheet
   60     72   H alpha helix
   78     81   E beta sheet
   85     97   H alpha helix
  101    104   E beta sheet
  117    119   E beta sheet
  128    136   H alpha helix
  142    148   E beta sheet
  151    166   H alpha helix
  170    177   E beta sheet
  183    196   H alpha helix
  200    204   E beta sheet
  208    221   H alpha helix
  229    231   E beta sheet
  236    239   H alpha helix
  244    247   H alpha helix
  251    254   E beta sheet
  263    273   H alpha helix
  284    303   H alpha helix
  308    315   H alpha helix
  320    322   E beta sheet
  325    329   E beta sheet
  336    337   E beta sheet
  341    345   E beta sheet
  351    356   E beta sheet
You are advised to use several of the latest Web-based prediction sites and combine them to make a consensus prediction.
This application was modified for inclusion in EMBOSS by