Here is a sample session with garnier. I don't remember what they are, but I must have gotten the values from their paper. Input file format Any protein sequence. Output file format Here is the output from the example run. TTT T coil CCC CCC C CCC C CCCC CC .
Data files None.
The Garnier method is not regarded as the most accurate prediction, but is simple to calculate on most workstations. The Web servers for PHD, DSC, and others are generally preferred. 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. You are advised to use several of the latest Web-based prediction sites and combine them to make a consensus prediction.