The CAST algorithm is described in a paper published in Bioinformatics
Vasilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy,
Stavros J. Hamodrakas, Chris Sander, and Christos A. Ouzounis
CAST: an iterative algorithm for the complexity analysis of sequence tracts
Bioinformatics (2000), 16(10), 915-922.
(View OnLine Abstract)
CAST is a novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.