We list some of the software needed to analyse a single protein sequence. The list is by no means complete. This program, analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc. One of its options is to generate self-explanatory output. Dot-plotting is the best way to visualize all of the repeated or inverted repeated structures in one sequence or to see all of the structures in common between two sequences.
Repeat finds direct repeats in sequences.
The PredictProtein Server PredictProtein Database Searches and predictions of secondary structure, residue solvent accessibility, transmembrane helix location, protein globularity, coiled-coil regions. Unix Membrane TMAP PHDhtm - TMAP predicts transmembrane segments in proteins. Isoelectric calculates the isoelectric point of a protein from its amino acid composition assuming no electrostatic interactions occur that perturb ionization.