Scoring matrix

In this equation, whereas the same loading matrix (YT matrix) is common for the different individual data matrices Dt, k = 1, 2, 3, 4, four different score matrices Xjt, k = 1, 2, 3, 4 are considered to explain the variation in Daug. Since these four D. matrices have equal sizes (same number of rows or samples and of columns or variables) they can also be arranged in a three-way data cube, with the four data matrices in the different slabs of this cube. However, in the frame of the MCR-ALS method and of the general bilinear model in (10), it is preferable to consider them to be arranged in the column-wise augmented data matrix Daug. 

In the case of data following a trilinear model structure [7], the profiles in the score matrices X in Xaug of (10) will present the same shape in the score profiles (or, in other words, the relative distribution of contamination patterns among samples in the different data matrices is the same) in the different individual data matrices D (obtained in the different sampling campaigns). In this case, the data set fulfills the trilinear model [7, 15, 21], which can be described by (11) (in this equation, superindex t in D k and X k matrices indicates that they conform to the trilinear model) ... 

Proteins Using Position-Specific Scoring Matrices. 248... 

IMPALA matching a protein sequence against a collection of PSI-BLAST-constructed position-specific scoring matrices. Bioinformatics, in press. 

Jones, D. T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. 

Muller T, Rahmann S, Rehmsmeier M. Nonmmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 2001 17(suppl 1) S182-S189. 

Gowri VS, Krishnadev O, Swamy CS et al (2006) MulPSSM a database of multiple position-specific scoring matrices of protein domain families. Nucleic Acids Res 34 D243-D246... 

Each scores matrix consists of a series of column vectors, and each loadings matrix a series of row vectors. Many authors denote these vectors by ta and pa, where a is the number of the principal component (1, 2, 3 up to A). The scores matrices T and P are composed of several such vectors, one for each principal component. The first... 

Perform PCA to give loadings and scores matrices T and P for the x data, then obtain a vector r for the c data using standard regression techniques. Note that these arrays will differ according to which sample is removed from the analysis. 

Figure 4.1. The matrix relationships in PLS as shown by [67]. T and U are PLS scores matrices of X and Y blocks, respectively, P contains the X loadings, W and Q are weight matrices for X and Y blocks, respectively, and E and F are residual matrices of X and Y blocks.

Consensus of several profile alignment methods with different scoring matrices and profiles... 

Henikoff, J. G. and S. Henikoff, Using substitution probabilities to improve position-specific scoring matrices. ComputAppl Biosci, 1996. 12(2) p. 135-43. 

Panchenko, A. R. and Bryant, S. H. (2002) A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci. 11, 361-370. 

Frith, M. C., Spouge, J. L., Hansen, U., and Weng, Z. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res. 30, 3214-3224. 

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