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is its (unimodular) substitution matrix. The family

by Markus Moll
"... 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. ..."
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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 well-known 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

by Sutormin R. A, Rakhmaninova A. B
"... 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

by Xin Liu - 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 matri-ces derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
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.

A protein structural alphabet and its substitution matrix CLESUM

by Wei-mou Zheng, Xin Liu , 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 coarse-gra ..."
Abstract - Cited by 5 (1 self) - Add to MetaCart
-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

by unknown authors
"... 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 consequent ..."
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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

Relation between weight matrix and substitution matrix: Motif search by similarity

by Wei-mou Zheng
"... Motivation: The discovery of patterns shared by several sequences that differ greatly is a basic task in se-quence analysis, and still a challenge. Several methods have been developed for detecting patterns. Methods commonly used for motif search include the Gibbs sampler, Expectation-Maximization ( ..."
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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 non-specific DNA microarray hybridization

by Aron C. Eklund, Pia Friis, Rasmus Wernersson, Zoltan Szallasi , 2009
"... DNA microarray measurements are susceptible to error caused by non-specific hybridization between a probe and a target (cross-hybridization), or between two targets (bulk-hybridization). Search algorithms such as BLASTN can quickly identify potentially hybridizing sequences. We set out to improve BL ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
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

Substitution Matrix Based Kernel Functions for Protein Secondary Structure Prediction

by Bram Vanschoenwinkel, Bernard Manderick - 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 ..."
Abstract - Cited by 10 (3 self) - Add to MetaCart
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

by Uros Midic, A. Keith Dunker, Zoran Obradovic
"... 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.

by Pierre Collin-Dufresne , Robert S Goldstein , J Spencer Martin , Gurdip Bakshi , Greg Bauer , Dave Brown , Francesca Carrieri , Peter Christoffersen , Susan Christoffersen , Greg Duffee , Darrell Duffie , Vihang Errunza , Gifford Fong , Mike Gallmeyer , Laurent Gauthier , Rick Green , John Griffin , Jean Helwege , Kris Jacobs , Chris Jones , Andrew Karolyi , Dilip Madan , David Mauer , Erwan Morellec , Federico Nardari , N R Prabhala , Tony Sanders , Sergei Sarkissian , Bill Schwert , Ken Singleton , Chester Spatt , René Stulz - 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 ..."
Abstract - Cited by 422 (2 self) - Add to MetaCart
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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