SAPS

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).

Installed on the Opteron Cluster.

Opteron version May 11, 1993

The SAPS executable is in /home/biomed/bin/.

SAPS users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.

Usage:

saps [arguments]

Other SAPS information:

  • Usage guide, which describes options and parameters.

  • Reference: Brendel, V., Bucher, P., Nourbakhsh, I., Blaisdell, B.E., Karlin, S. (1992) "Methods and Algorithms for statistical analysis of protein sequences." Acad. Sci. USA 89: 2002-2006.

  • For the most recent version of the software, please contact the SAPS supplier.

See also: