List Linear n-Peptide Constraints for Overlapping Protein Regions

Share:

Description

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

Author(s)

S. Lebre

Maintainer: S. Lebre <sophie.lebre@umontpellier.fr>

References

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

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
	## 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)