DCODE (version 1.0)

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

Description

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

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)