protein

Documentation

Index

• Constants
• Variables
• func ABMats() (dmat *mat.Dense, pi []float64)
• func DayoffMats() (dmat *mat.Dense, pi []float64)
• func HIVBMats() (dmat *mat.Dense, pi []float64)
• func JTTMats() (dmat *mat.Dense, pi []float64)
• func LGMats() (dmat *mat.Dense, pi []float64)
• func ModelStringToInt(model string) int
• func MtREVMats() (dmat *mat.Dense, pi []float64)
• func WAGMats() (dmat *mat.Dense, pi []float64)
• type ProtModel
  • func NewProtModel(model int, usegamma bool, alpha float64) (*ProtModel, error)
  • func (model *ProtModel) Alpha() float64
  • func (model *ProtModel) Analytical() bool
  • func (model *ProtModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (model *ProtModel) Eval() (val []float64)
  • func (model *ProtModel) InitModel(aafreqs []float64) error
  • func (model *ProtModel) LeigenVects() (leftvectors *mat.Dense)
  • func (model *ProtModel) NState() int
  • func (model *ProtModel) Pi(i int) float64
  • func (model *ProtModel) Pij(i, j int, l float64) float64
  • func (model *ProtModel) PrintFreqs()
  • func (model *ProtModel) PrintMat()
  • func (model *ProtModel) ReigenVects() (rightvectors *mat.Dense)
  • func (model *ProtModel) UseGamma() bool

Constants

const (
	MODEL_DAYHOFF = iota
	MODEL_JTT
	MODEL_MTREV
	MODEL_LG
	MODEL_WAG
	MODEL_HIVB
	MODEL_AB

	BL_MIN  = 1.e-08
	BL_MAX  = 100.0
	DBL_MIN = 2.2250738585072014e-308
)

Variables

var DBL_EPSILON float64 = math.Nextafter(1, 2) - 1

Functions

func ABMats

func ABMats() (dmat *mat.Dense, pi []float64)

Antibody-Specific Model of Amino Acid Substitution From AB Model publication (supplementary material online) Alexander Mirsky, Linda Kazandjian, Maria Anisimova, Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences, Molecular Biology and Evolution, Volume 32, Issue 3, March 2015, Pages 806–819, https://doi.org/10.1093/molbev/msu340

func DayoffMats

func DayoffMats() (dmat *mat.Dense, pi []float64)

Dayhoff's model data * Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978) * "A model of evolutionary change in proteins." * Dayhoff, M.O.(ed.) Atlas of Protein Sequence Structur., Vol5, Suppl3. * National Biomedical Research Foundation, Washington DC, pp.345-352.

func HIVBMats

func HIVBMats() (dmat *mat.Dense, pi []float64)

From PhyML code Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL. HIV-Specific Probabilistic Models of Protein Evolution. PLoS ONE. 2007 Jun 6;2:e503. [thanks to Sergei L. Kosakovsky] Translated from HYPHY to Phyml format by Federico Abascal.

func JTTMats

func JTTMats() (dmat *mat.Dense, pi []float64)

JTT's model data * D.T.Jones, W.R.Taylor and J.M.Thornton * "The rapid generation of mutation data matrices from protein sequences" * CABIOS vol.8 no.3 1992 pp275-282

func LGMats

func LGMats() (dmat *mat.Dense, pi []float64)

LG model * Si Quang LE & Olivier Gascuel * "An improved general amino-acid replacement matrix" * Mol Biol Evol. 2008 Jul;25(7):1307-20.

func ModelStringToInt

func ModelStringToInt(model string) int

Returns code of the model If the model does not exist, returns -1

func MtREVMats

func MtREVMats() (dmat *mat.Dense, pi []float64)

Model of amino acid substitution in proteins encoded by mitochondrial DNA Jun Adachi & Masami Hasegawa Mol Evol 42, 459–468 (1996) https://doi.org/10.1007/bf02498640

func WAGMats

func WAGMats() (dmat *mat.Dense, pi []float64)

WAG's model data * Simon Whelan and Nick Goldman * "A general empirical model of protein evolution derived from multiple * protein families using a maximum-likelihood approach" * MBE (2001) 18:691-699

Types

type ProtModel

type ProtModel struct {
	// contains filtered or unexported fields
}

func NewProtModel

func NewProtModel(model int, usegamma bool, alpha float64) (*ProtModel, error)

Initialize a new protein model, given the name of the model as const int: MODEL_DAYHOFF, MODEL_JTT, MODEL_MTREV, MODEL_LG, MODEL_WAG or MODEL_HIVB

func (*ProtModel) Alpha

func (model *ProtModel) Alpha() float64

func (*ProtModel) Analytical

func (model *ProtModel) Analytical() bool

func (*ProtModel) Eigens

func (model *ProtModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

func (*ProtModel) Eval

func (model *ProtModel) Eval() (val []float64)

func (*ProtModel) InitModel

func (model *ProtModel) InitModel(aafreqs []float64) error

Initialize model with given aa frequencies If aafreqs is nil, then uses model frequencies

func (*ProtModel) LeigenVects

func (model *ProtModel) LeigenVects() (leftvectors *mat.Dense)

func (*ProtModel) NState

func (model *ProtModel) NState() int

func (*ProtModel) Pi

func (model *ProtModel) Pi(i int) float64

func (*ProtModel) Pij

func (model *ProtModel) Pij(i, j int, l float64) float64

func (*ProtModel) PrintFreqs

func (model *ProtModel) PrintFreqs()

func (*ProtModel) PrintMat

func (model *ProtModel) PrintMat()

func (*ProtModel) ReigenVects

func (model *ProtModel) ReigenVects() (rightvectors *mat.Dense)

func (*ProtModel) UseGamma

func (model *ProtModel) UseGamma() bool