SAPS (Statistical Analysis of Protein Sequences) evaluates by statistical criteria a wide variety of protein sequence properties. Properties considered include
  compositional biases
  clusters and runs of charge and other amino acid types
  different kinds and extents of repetitive structures
  locally periodic motifs
  and anomalous spacings between identical residue types

The statistics are computed for any single (or appropriately concatenated) protein sequence input. Statistically significant sequence features highlighted by SAPS in the input sequence may suggest promising regions for experimental investigation. The program also finds application in the description of conserved features of families of proteins as well as in the inverse problem of deriving protein groupings based upon sequence features.

Short sequences are subject to larger statistical fluctuations than longer sequences. The statistical evaluations of SAPS are reliable only for sequences of at least about 200 residues. Shorter sequences may in some cases be appropriately concatenated and analyzed as a representative combined sequence (e.g., histones, or Ras family proteins).