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DayMatrix

Class DayMatrix - similarity scoring matrix or Dayhoff matrix

Calling Sequence DayMatrix(PAM)
CreateDayMatrix(logPAM1,PAM)
CreateDayMatrices()
CreateOrigDayMatrix()

Selectors

Name	Type	Description

`DelCost`	procedure	proc(k,pam) gives cost of k-long indel
`Dimension`	posint	dimension of the similarity matrix
`FixedDel`	numeric	fixed cost (opening) for affine indels
`IncDel`	numeric	incremental cost for affine indels
`logPAM1`	matrix	rate matrix used for this DayMatrix
`Mapping`	procedure	proc to map symbols to matrix indices
`MaxOffDiag`	numeric	maximum similarity for distinct residues
`MaxSim`	numeric	maximum similarity score in the matrix
`MinSim`	numeric	minimum similarity score in the matrix
`PamDistance`	numeric	PAM distance of this matrix
`PamNumber`	numeric	PAM distance of this matrix
`Sim`	matrix(numeric)	Similarity matrix of scores (see below)
`StopSimil`	numeric	cost of matching a stop codon
`type`	symbol	type of scoring matrix, Peptide or Nucleotide

Methods print

Synopsis A DayMatrix is the data structure or class which holds similarity scores computed from mutation matrices. The matrices are used for alignment of sequences. The scores have a precise mathematical meaning: they are 10 times the log10 of the probability that the alignment comes from homology as opposed to a random coincidence. Hence alignment scores give a rough estimate of how rare the alignment is if it were produced by chance only. The functions which create DayMatrices (CreateDayMatrices) normally assign a dense array of DayMatrix to the variable DMS (to allow estimation of distances between sequences) and a 250-PAM matrix to DM (the most commonly used matrix). Currently, DayMatrices are internal objects. The functions mentioned in the Template part above are used to create DayMatrices. Some other commonly used scoring matrices can be obtained by the command Matrices(). When DayMatrix is used as a constructor (first entry above), it searches the list of DayMatrix DMS for a matrix of the right PAM and returns it. If none is found, it calls CreateDayMatrix to build an appropriate one.

When selecting the similarity matrix from a DayMatrix (selector Sim), a new matrix is constructed and returned. If the selection on Sim is immediately followed by two indices, then no matrix is constructed and the corresponding entry of the Dayhoff matrix is returned. For this special case, (e.g. DM[Sim,a,b]), the selectors a and b can be the one letter codes for the amino acids. This is more efficient and simpler than invoking the AToInt conversion.

Examples

> CreateDayMatrices();

> DM[Sim,1,1];

2.3562

> DMS[100,Sim,L,I];

-17.8435

> DayMatrix(316);

DayMatrix(Peptide, pam=316, Sim: max=12.964, min=-3.989, del=-19.057-1.396*(k-1))

See also CreateDayMatrices, CreateDayMatrix, CreateOrigDayMatrix, Matrices, SearchDayMatrix