2002/04/05 by Miguel Angel Jimenez-Montano, Werner Ebeling, Thorsten Poeschel · 2 citations
Physics and Astronomy · Biochemistry, Genetics and Molecular Biology · #cond-mat.dis-nn #q-bio.QM
published as In: R. Lopez-Pena, H. Waelbroeck und F. Zertuche (eds.), Guanajuato Lectures, Mexico, 16 - 22 Januar 1995, Springer, New York · 11 pages
arxiv created 2002/04/05 · arxiv updated 2009/11/30
The determination of block-entropies is a well established method for the investigation of discrete data, also called symbols (7). There is a large variety of such symbolic sequences, ranging from texts written in natural languages, computer programs, neural spike trains, and biosequences. In this paper a new algorithm to construct a short context-free grammar (also called program or description) that generates a given sequence is introduced. It follows the general lines of a former algorithm, employed to compress biosequences (1,2) and to estimate the complexity of neural spike trains (4), which uses as valuation function the, so called, grammar complexity (2). The new algorithm employs the (observed) block-entropies instead. A variant, which employs a corrected "observed entropy", as discussed in (7) is also described. To illustrate its usefulness, applications of the program to the syntactic analysis of a sample biological sequences (DNA and RNA) is presented.