In 1989, Godrèche and Luck [1] introduced the concept of local mixtures of primitive substitution rules along the example of the well-known Fibonacci substitution and foreshadowed heuristic results on the topological entropy and the spectral type of the diffraction measure of associated point sets

Key words: comparative analysis, bacterial transporters, amino acid substitution matrix

in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational seg-ment search and homolog detection.

-graining procedure converts a 3D structure to a 1D code sequence. A substitution matrix between these letters is constructed based on the structural alignments of the FSSP database. Key words: structure alignment; structural codes; structural substitution matrix. 1

Glycans are chains of monosaccharides, known to be extremely vital for the development and functioning of multi-cellular organisms. Matching and alignment algorithms for glycans were introduced based on proven efficient methods in bioinformatics for protein sequences [2]. These algorithms consequently can be taken advantage of in the form of statistical analyses. These algorithms were designed

model describing a motif or a portion of local multiple sequence alignment is the weight matrix model, in which a motif is characterized with position specific probabilities. Two substitution matrices are proposed to relate the sequence similarity with the weight matrix. Combining the substitution

BLASTN accuracy by modifying the substi-tution matrix and gap penalties. We generated gene expression microarray data for samples in which 1 or 10 % of the target mass was an exogenous spike of known sequence. We found that the 10 % spike induced 2-fold intensity changes in 3 % of the probes, two

of a substitution matrix (SM), i.e. a matrix that contains evolutionary information about the substitutability of the different amino acids that make up proteins. The starting point is always the same, i.e. a pseudo inner product (PI) between amino acid sequences making use of a SM. It is shown what

In protein sequence alignment algorithms, a substitution matrix of 20x20 alignment parameters is used to describe the rates of amino acid substitutions over time. Development and evaluation of most substitution matrices including the BLOSUM family [1] was based almost entirely on fully structured

observations with actual quotes are used, since it has been shown by Sarig and Warga (1989) that matrix prices are problematic. 10 To determine the credit spread, CS i t , for bond i at month t, we use the Benchmark Treasury rates from Datastream for maturities of 3, 5, 7, 10, and 30 years, and then use a