getConstraint: Function giving the linear constraint associated with the...

In DCODE: List Linear n-Peptide Constraints for Overlapping Protein Regions

Description

This function prints the linear constraint to which the chosen peptide in the reference frame pep is subject when condisering gene overlap with frameshift frame.

Usage

getConstraint(pep, frame, code, pepList)

Arguments

pep	A chosen n-peptide in the reference frame (with length n<=5 if pepList is generated by function build_data).
frame	The frameshift chosen in {-2, -1, 0, 1, 2}.
code	The code used to translate codons into amino acids (which can be generated by function build_data).
pepList	A list of all the peptide of length 1, 2, 3, ...required by the graph traversal algorithm (which can be generated by function build_data).

Author(s)

Sophie Lebre <[e-mail]>

References

Lebre and Gascuel, The combinatorics of overlapping genes (freely available from arXiv at:

http://arxiv.org/abs/1602.04971).

See Also

build_data

Examples

	## Not run: 
# 1) Build peptideList, used by function getConstraint.
mydata <- build_data()
aaList <- mydata$aaList
geneticCode <- mydata$geneticCode
peptideList <- mydata$peptideList

# 2) Ask for the constraint induced on a chosen peptide in a chosen overlapping frame

## amino acid contraints 
getConstraint("C", frame = -2, code=geneticCode, pepList=peptideList) 
getConstraint("D", frame = 1, code=geneticCode, pepList=peptideList)

## 3-peptide contraints
getConstraint("CWC",frame = -2, code=geneticCode, pepList=peptideList)

## 5-peptide contraints
getConstraint("CWCCC",frame = -2, code=geneticCode, pepList=peptideList)
	
## End(Not run)

Example output

Loading required package: seqinr
[1] "Initialization..."
[1] "CAPITAL LETTERS and small letters denote respectively peptides read in the REFERENCE frame and the overlapping frame."
[1] "C + W  =  h + q"
[1] "CAPITAL LETTERS and small letters denote respectively peptides read in the REFERENCE frame and the overlapping frame."
[1] "D + H + N + Y  =  i + m + t"
[1] "CAPITAL LETTERS and small letters denote respectively peptides read in the REFERENCE frame and the overlapping frame."
[1] "CWC + CWW  =  hqh + hqq"
[1] "CAPITAL LETTERS and small letters denote respectively peptides read in the REFERENCE frame and the overlapping frame."
[1] "CWCCC + CWCCW  =  qqhqh + qqhqq"

DCODE documentation built on May 1, 2019, 6:49 p.m.