Description Usage Value Author(s) References See Also Examples
To be run before the first use of function getConstraint
.
This function generates the variables aaList
, geneticCode
and peptideList
, a list of all the peptides (up to length 5), used by function getConstraint
.
1 |
aaList |
Vector of all amino acids. |
geneticCode |
A list describing the standard genetic code. |
peptideList |
A list of all the peptides (up to length 5). |
Sophie Lebre <sophie.lebre@umontpellier.fr>
Lebre and Gascuel, The combinatorics of overlapping genes (freely available from arXiv at:
http://arxiv.org/abs/1602.04971).
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)
|
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"
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.