How can I compare the STRIDE and DSSP output files of a particular pdb file?
Here a solution that does not require you to upload the files to the servers: You can graphically visualize DSSP and Stride at the Sequence Page at RCSB PDB:

http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=5P21&amp;bionumber=1

"add annotation" -> Stride and look at the graphical comparison between DSSP and Stride.