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is its (unimodular) substitution matrix. The family
"... In 1989, Godrèche and Luck [1] introduced the concept of local mixtures of primitive substitution rules along the example of the wellknown Fibonacci substitution and foreshadowed heuristic results on the topological entropy and the spectral type of the diffraction measure of associated point sets. ..."
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In 1989, Godrèche and Luck [1] introduced the concept of local mixtures of primitive substitution rules along the example of the wellknown Fibonacci substitution and foreshadowed heuristic results on the topological entropy and the spectral type of the diffraction measure of associated point sets
BATMAS30 THE AMINO ACID SUBSTITUTION MATRIX FOR ALIGNMENT OF BACTERIAL TRANSPORTERS
"... Key words: comparative analysis, bacterial transporters, amino acid substitution matrix ..."
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Key words: comparative analysis, bacterial transporters, amino acid substitution matrix
An amino acid substitution matrix for protein conformation identification
 Journal of bioinformatics and computational biology
, 2006
"... Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation ..."
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in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformationspecific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.
A protein structural alphabet and its substitution matrix CLESUM
, 2004
"... To whom correspondence should be addressed. By using a mixture model for the density distribution of the three pseudobond angles formed by Cα atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural alphabet. This coarsegra ..."
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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
Glycan Linkage Substitution Matrix Rooted on Tree Alignments
"... Glycans are chains of monosaccharides, known to be extremely vital for the development and functioning of multicellular organisms. Matching and alignment algorithms for glycans were introduced based on proven efficient methods in bioinformatics for protein sequences [2]. These algorithms consequent ..."
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Glycans are chains of monosaccharides, known to be extremely vital for the development and functioning of multicellular 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
Relation between weight matrix and substitution matrix: Motif search by similarity
"... Motivation: The discovery of patterns shared by several sequences that differ greatly is a basic task in sequence analysis, and still a challenge. Several methods have been developed for detecting patterns. Methods commonly used for motif search include the Gibbs sampler, ExpectationMaximization ( ..."
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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
Optimization of the BLASTN substitution matrix for prediction of nonspecific DNA microarray hybridization
, 2009
"... DNA microarray measurements are susceptible to error caused by nonspecific hybridization between a probe and a target (crosshybridization), or between two targets (bulkhybridization). Search algorithms such as BLASTN can quickly identify potentially hybridizing sequences. We set out to improve BL ..."
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BLASTN accuracy by modifying the substitution 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 2fold intensity changes in 3 % of the probes, two
Substitution Matrix Based Kernel Functions for Protein Secondary Structure Prediction
 In Proceedings of ICMLA04 (International Conference on Machine Learning and Applications
, 2004
"... Different approaches to using substitution matrices in kernel functions for protein secondary structure prediction (PSSP) with support vector machines are investigated. This work introduces a number of kernel functions that calculate inner products between amino acid sequences based on the entries o ..."
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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
Protein Sequence Alignment and Structural Disorder: A Substitution Matrix for an Extended Alphabet
"... 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 pr ..."
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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
The Determinants of Credit Spread Changes.
 Journal of Finance
, 2001
"... ABSTRACT Using dealer's quotes and transactions prices on straight industrial bonds, we investigate the determinants of credit spread changes. Variables that should in theory determine credit spread changes have rather limited explanatory power. Further, the residuals from this regression are ..."
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Cited by 422 (2 self)
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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
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