TKF92: Evolutionary distance estimation with TKF92 model

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/TKF92.R

Description

This function implements the TKF92 model to estimate the pairwise distance from protein sequences.

Usage

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TKF92(fasta, mu=NULL, r=NULL, expectedLength=362, 
      substModel, substModelBF)
TKF92Pair(seq1, seq2, mu=NULL, r=NULL, distance=NULL,
          expectedLength=362, substModel, substModelBF)

Arguments

fasta

A named list of sequences in vector of characters format. read.fasta from package seqinr outputs this format when reading from a fasta file.

mu

A numeric value between 0 and 1 or NULL. It is the death rate per normal link in TKF92 model. When it is NULL, a joint estimation of mu, r and distance will be done. When it is given, only the distance will be estimated.

r

A numeric value between 0 and 1 or NULL. It is the success probability of the geometric distribution for modeling the fragment length in TKF92 model. When it is NULL, a joint estimation of mu, r and distance will be done. When it is given, only the distance will be estimated.

distance

A numeric value: the PAM distance between two protein sequences. When it is given, TKF92Pair only calculates the negative log-likelihood.

expectedLength

A numeric object: the expected length of input protein sequences. By default, the average sequence length, 362, from OMA browser is used.

substModel

A numeric matrix: the mutation probability from one AA to another AA at PAM distance 1. The order of AA in the matrix should be identical to AACharacterSet.

substModelBF

A vector of numeric: the backrgound frequency of AAs. The order of AA in the vector should also be identical to AACharacterSet.

seq1, seq2

A vector of character: the sequences of two proteins to compare.

Details

Currently this implementation only supports the normal 20 AAs. Missing or Ambiguous characters are not supported.

Value

A list of matrices are returned: the matrix of estimated distances, the matrix of estimated distance variances, the matrix of negative log-likelihood between the sequences.

Author(s)

Ge Tan

References

Thorne, J.L., Kishino, H., and Felsenstein, J. (1992). Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34, 3-16.

Gonnet, G.H., Cohen, M.A., and Benner, S.A. (1992). Exhaustive matching of the entire protein sequence database. Science 256, 1443-1445.

See Also

AACharacterSet, GONNET, GONNETBF

Examples

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    ## This example is not tested due to running time > 5s
  data(GONNET)
  data(GONNETBF)
  library(seqinr)
  fasta <- read.fasta(file.path(system.file("extdata", package="TKF"),
                      "pair1.fasta"),
                      seqtype="AA", set.attributes=FALSE)
  ## 1D estimation: only distance
  TKF92(fasta, mu=0.0006137344, r=0.7016089061,
        substModel=GONNET, substModelBF=GONNETBF)
  
  ## 2D estimation: joint estimation of distance, mu and r
  TKF92(fasta, substModel=GONNET, substModelBF=GONNETBF)
  
  ## only apply to a pair of sequences
  seq1 <- fasta[[1]]
  seq2 <- fasta[[2]]
  TKF92Pair(seq1, seq2, mu=0.0006137344, r=0.7016089061,
            substModel=GONNET, substModelBF=GONNETBF)
  

TKF documentation built on May 29, 2017, 9:37 p.m.

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