seqinr (version 1.0-1)

plot.SeqAcnucWeb: To Plot Subsequences on the Parent Sequence

Description

This function allows to plot all the type of subsequences on a parent sequence.Subsequences are represented by colored rectangle on the parent sequence. As an example, types could be CDS, TRNA, RRNA .... In order to get all the types that are available for the selected database, please run getType.socket.

Usage

plot.SeqAcnucWeb(x, type = "all", ...)

Arguments

x

A sequence of class SeqAcnucWeb

type

The type of subsequences to plot. if all, all the type of subsequences will be drawn.

...

graphical parameters can also be specified as arguments

Value

• The plot. A list giving, for each subsequence, its position on the parent sequence.

References

http://pbil.univ-lyon1.fr/databases/acnuc.html

To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

See Also

getType, query

Examples

s=choosebank("hovernucl")
query(s$socket,"list","sp=homo sapiens et k=globin@")	
plot.SeqAcnucWeb(list$req[[22]])
plot.SeqAcnucWeb(list$req[[22]],type=c("CDS","5'NCR"))