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	Substitution matrix - Wikipedia, the free encyclopedia
		Substitution matrices are usually seen in the context of amino acid or DNA sequence alignment, where the similarity between sequences depends on the mutation rates as represented in the matrix.
		The simplest possible substitution matrix would be one in which each amino acid is considered maximally similar to itself, but not able to transform into any other amino acid.
		One of the first amino acid substitution matrices, the PAM (Percent Accepted Mutation) matrix was developed by Margaret Dayhoff in the 1970s.
	en.wikipedia.org /wiki/Substitution_matrix (949 words)

	Folding@Home Educational Project (Site not responding. Last check: 2007-10-09)
		Substitution The presence of a non-identical amino acid at a given position in an alignment.
		Substitution Matrix A substitution matrix containing values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids.
		The BLOSUM 62 matrix shown here is a 20 x 20 matrix of which a section is shown here in which every possible identity and substitution is assigned a score based on the observed frequencies of such occurences in alignments of related proteins.
	folding.stanford.edu /education/s.html (323 words)

	Substitution matrix (Site not responding. Last check: 2007-10-09)
		Substitution matrices are usually in the context of protein or DNA sequence alignment.
		To this end we will construct a matrix where the $(i j) th entry is to the probabiliy of the i th amino being transformed into the j th amino acid a certain amount of evolutionary time.$
		The simplest possible substitution matrix would be in which each amino acid is considered similar to itself but not able to into any other amino acid.
	www.freeglossary.com /Substitution_matrix (916 words)

	Environmental and Health Assessment of Alternatives to Phthalates and to flexible PVC, Danish Environmental Protection ...
		Estimation of exposure in a future substitution scenario was attempted by establishing a 'realistic' use pattern scenario for all the substitutes in PVC applications.
		The input data for the calculation are the substitution matrix and scenarios with the largest estimated consumption substitute for phthalate plasticisers.
		In the 100% substitution case it is chosen to base the estimates on the most recent inventory of the phthalates in PVC and use the sum used in 1992 (10,735 tons).
	www.mst.dk /udgiv/publications/2001/87-7944-407-5/html/helepubl_eng.htm (9254 words)

	Matrix and Gap Costs
		A key element in evaluating the quality of a pairwise sequence alignment is the "substitution matrix", which assigns a score for aligning any possible pair of residues.
		The theory of amino acid substitution matrices is described in [1], and applied to DNA sequence comparison in [2].
		In general, different substitution matrices are tailored to detecting similarities among sequences that are diverged by differing degrees [1-3].
	www.genome.ou.edu /blast/docs/matrix_info.html (640 words)

	Northwestern Oklahoma State University - Learn today, lead tomorrow
		Substitutions from within the state matrix system should be approved automatically, requiring no application.
		For course substitutions the student should provide course syllabus and university catalog from the institution in which the course being used for the substitution was originally taken for credit.
		To be justified as a substitution the course should have similar content and required skills throughout the entire course.
	www.nwosu.edu /catalog/index.html (493 words)

	seqaln-intro man page
		Sequence files are specified in the Pearson/FASTA format and substitution matrix files are in BLAST format, allowing users to employ sequences and substitution matrices directly available from the NCBI.
		This differs from the penalty matrix versions (see the matrix option below), where one score is assigned to a given letter match regardless of its position in the sequence.
		Programs that use a substitution matrix (i.e., those beginning with `m') use parameter matrix as the name of the substitution score matrix file.
	bioweb.pasteur.fr /docs/seqaln/seqaln-intro.1.html (2386 words)

	Substitution matrix - InformationBlast
		Substitution matrices are usually seen in the context of protein or DNA sequence alignment.
		To this end, we will construct a 20x20 matrix where the (i,j)th entry is equal to the probabiliy of the ith amino acid being transformed into the jth amino acid in a certain amount of evolutionary time.
		One of the first amino acid substitution matrices, the PAM matrix was developed by Dayhoff in the 1970s.
	www.informationblast.com /Substitution_matrix.html (664 words)

	cb_swa_fw(3B) Last changed: 03-27-03 (Site not responding. Last check: 2007-10-09)
		The substitution scores and the extend gap penalty, eg, and the open gap penalty, og, are used to compute the Smith-Waterman aligment of the two strings.
		cb_swa_fw_init accepts two strings, dbl and dbs, and a substitution score lookup table, sslookup, and fills the table swtab with the substitution scores in rows and columns corresponding to the entries in the dbs and dbl strings.
		sslookup(i,j) (Fortran) or sslookup[j][i] (C) is the substitution score for data entities represented by the i'th and j'th letters of the alphabet or packed nucleotide codes equal to i and j.
	www.sanbi.ac.za /Cray/cb_swa_fw.html (1212 words)

	FORCASP - CASP Forums Site - Probabilistic Fragments, Optimized Substitution Matrices And Fold Recognition (Wurst)
		This weighting was also treated as a parameter to be optimized and even the 210 elements of an amino acid substitution matrix were treated as parameters to be optimized.
		To this end, an optimization was carried out of all gap penalties, the substitution matrix and the weights of the different terms simultaneously.
		It also produced a substitution matrix which was too highly tuned to sequences with a large number of close sequence homologues.
	www.forcasp.org /print/2210 (715 words)

	substitution reaction - Hutchinson encyclopedia article about substitution reaction (Site not responding. Last check: 2007-10-09)
		In chemistry, the replacement of one atom or functional group in an organic molecule by another.
		Substitution Failure Is Not An Error (C++ templates)
		This information should not be considered complete, up to date, and is not intended to be used in place of a visit, consultation, or advice of a legal, medical, or any other professional.
	encyclopedia.farlex.com /substitution%20reaction (85 words)

	The compositional adjustment of amino acid substitution matrices -- Yu et al. 100 (26): 15688 -- Proceedings of the ...
		matrix to frequencies appropriate for a nonstandard context.
		Although a substitution matrix is valid in the context of the
		of a substitution matrix is its relative entropy (2, 10).
	www.pnas.org /cgi/content/full/100/26/15688 (3272 words)

	BioMed Central \| Full text \| EvDTree: structure-dependent substitution profiles based on decision tree classification ...
		To derive structure-dependent substitution matrices, multiple sequence alignments are also needed as well as a description of the 3D structure at each position in the alignment [15,17].
		This matrix, referred to as EvDTree0, is simply derived from the structural superimpositions in the learning data set and is thus similar to other structure-derived substitution matrices [36].
		Comparison with structure-dependent substitution matrices obtained by other groups is not as simple as for standard substitution matrices, because we must make sure that we compute the structural environment exactly the same way that was used for generating the matrices.
	www.biomedcentral.com /1471-2105/6/4 (8361 words)

	Substitution Matrices (Site not responding. Last check: 2007-10-09)
		The PAM1 is the matrix calculated from comparisons of sequences with no more than 1% divergence.
		BLOSUM 62 is a matrix calculated from comparisons of sequences with no less than 62% divergence.
		If distant relatives of the query sequence are specifically being sought, the matrix can be tailored to that type of search.
	www.ncbi.nlm.nih.gov /Education/BLASTinfo/Scoring2.html (226 words)

	Structure derived substitution matrices (Site not responding. Last check: 2007-10-09)
		Amino acid substitution matrices for alignment of distantly related sequences have been derived using superimpositions from protein pairs of similar structure, but of low or no sequence similarity.
		One matrix was derived using original eight secondary structure states assignment by DSSP, another using three states.
		In the data set used such helices were not substituted to all other secondary structure elements, so they are excluded from the eight state matrix.
	lore.came.sbg.ac.at /Services/MATRICES/matrices.html (274 words)

	A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation -- Tanay et al. 14 (5): 829 -- Genome ...
		A family in the selection network is a cluster of motifs that are interconnected via high or neutral substitution rate arcs.
		The number inside the cell indicates the substitution rate when the neighbor has the nucleotide associated with the row in the position associated with the column, and all other motif nucleotides are unchanged.
		On the other hand, several substitutions that lead to the consensus appear with high rates, suggesting the possibility of motif optimization toward the preferable binding site.
	www.genome.org /cgi/content/full/14/5/829 (3487 words)

	Parameters
		Mutation energy describes the compatibility of substituting one amino acid by another in evolution.
		PROSPECT uses the PAM250 substitution matrix (data/parameters/gonnet.param) by default.
		Singleton energy represents a residue's local preference of secondary structures (helix, sheet, or loop) and its preference for a certain solvent environment (exposed to solvent or in the interior of the protein).
	compbio.ornl.gov /structure/prospect2/param.html (216 words)

	FORCASP - CASP Forums Site - Dunbrack (P0329) - 46 predictions: 46 3D
		The first is a Dirichlet mixture substitution matrix (DIMSUM) analogous to ordinary amino acid substitution matrices, but in which the scores represent probabilities of substituting profile columns for one another.
		The second scoring method is a combination of an amino acid substitution matrix and a matrix that represents the probability of predicted secondary structure in one profile (the CASP target) aligning to known secondary structure in the PDB entry.
		This matrix (SSAAC) was also developed from structure alignments by determining the substitution rates of predicted secondary structure in one protein in each structural alignment versus known secondary structure in the other protein.
	www.forcasp.org /modules.php?name=Papers&file=article&sid=1876 (325 words)

	Looping Constructs
		Let "A" be a (nxn) matrix, and "b" be a (nx1) matrix.
		In the method of LU decomposition, matrix "A" is decomposed into a product of lower and upper triangular matrices.
		Matrix functions are provided for the LU decomposition and forward/backward substitution.
	www.isr.umd.edu /~austin/aladdin.d/matrix-solve.html (682 words)

	Substitution Matrix Based Kernel Functions for Protein Secondary Structure Prediction - Vanschoenwinkel (ResearchIndex)
		Abstract: 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 of a substitution matrix (SM), i.e.
		Substitution matrix based kernel functions for protein secondary structure prediction.
	citeseer.ist.psu.edu /723055.html (428 words)

	[No title] (Site not responding. Last check: 2007-10-09)
		Substitution matrices are usually derived from multiple sequence alignments of proteins.
		The module SubsMat can be used in conjunction with those tools to easily generate a substitution matrix from an alignment.
		An example of substitution matrices generated from structural alignments of sequence dissimilar proteins will be shown, along with their analysis.
	www.open-bio.org /bosc2001/abstracts/lightning/friedberg (195 words)

	[No title]
		In a standard substitution matrix, such as BLOSUM62, the substitution of one amino acid with another is associated with a single score.
		Position-specific scoring matrix or HMMs profiles, in its simplest form, may consist of a set of 20 substitution scores at each position along the motif - one for each of the amino acids.
		The most probable path through the HMM (i.e., which transitions were taken and which residues were emitted at match and insert states) taken to generate a sequence similar to the new sequence determines the similarity score.
	www.sbc.su.se /~julian/hmm/hmms.html (494 words)

	Substitution Matrices (Site not responding. Last check: 2007-10-09)
		She and her coworkers developed a model of protein evolution which resulted in the development of a set of widely used substitution matrices.
		The number after the matrix (BLOSUM62) refers to the minimum percent identity of the blocks used to construct the matrix; greater numbers are lesser distances.
		If each matrix has its own limitations, then it should be possible to use multiple matrices so that each one complements the limits of the others.
	twod.med.harvard.edu /seqanal/submatrix.html (411 words)

	Gina Cannarozzi - Research (Site not responding. Last check: 2007-10-09)
		Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA.
		We presented the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA which provides an alternative to parameterized models of codon evolution.
		Because these substitutions are a stochastic process, time estimates are never precise but always subject to random variation.
	www.inf.ethz.ch /personal/cgina/research.html (594 words)

	Benefits of a Generalized Profile Syntax for Biomolecular Sequence Motifs
		The substitution matrix as well as the gap-scores are valid for all positions of the alignment.
		For the alignment of a profile to a sequence, no substitution matrix is needed, the information of the matrix is usually used in the construction of a profile.
		The simplest profile can thus be created from one sequence and one substitution matrix: the matrix is applied to each position of the sequence and gives a score for every possible residue in the alignment.
	www.isrec.isb-sib.ch /profile/chester94/chester94.html (2102 words)

	Directory of open access journals
		It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions.
		However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa.
		Substitution matrices found for sequences under selection pressure do not have this property.
	www.doaj.org /abstract?id=80743&toc=y (229 words)

	EMBOSS: dotmatcher (Site not responding. Last check: 2007-10-09)
		The score is the sum of the comparisons of the two sequences using the given similarity matrix along the window.
		It uses the specified matrix substitution file to compare the two sequences.
		For protein sequences EBLOSUM62 is used for the substitution matrix.
	www.agri.huji.ac.il /embossdocs/dotmatcher.html (550 words)

	A Simple Hierarchical Approach to Modeling Distributions of Substitution Rates -- Kosakovsky Pond and Frost 22 (2): 223 ...
		A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
		Nielsen, R. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA.
		A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences.
	mbe.oupjournals.org /cgi/content/full/msi009?ijkey=347SRkWDSgTnz&keytype=ref (4464 words)

	Assignment 1 (Site not responding. Last check: 2007-10-09)
		By mismatch before a gap I mean a diagonal move in the DP matrix before an orthogonal move.
		Using what we know about sequence alignment and dynamic programming suggest how we might write an algorithm to decide if a word is merely a misspelling of another word or is actually not the same word at all.
		Then by looking at these examples, deriving a substitution matrix using log odds ratios of reasonable substitutions for characters.
	marvin.ibest.uidaho.edu /~heckendo/CS504/pas1a.html (739 words)

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