DCODE-package: List Linear n-Peptide Constraints for Overlapping Protein...

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

Description

Traversal graph algorithm for listing linear n-peptide constraints for overlapping protein regions.

Author(s)

S. Lebre

Maintainer: S. Lebre <[e-mail]>

References

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

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

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.