[Seqinr-forum] Oriloc plot issues

[Daniel Bozinov]

Hi everyone,

I am using Oriloc in the seqinR package on various bacterial plasmids in 
fasta format. Some of them produce acceptable plots, however, a few 
others produce rather weird curves that I cannot explain. I could attach 
the actual images for illustration as well as the fasta files and 
corresponding glimmer prediction files, but I am not sure if file 
attachments are welcomed in this list. Therefore I will try to recreate 
the curve in question with ascii characters.

So an Oriloc plot could basically look something like this:

|
|
|              ___/\____
|             /            \
|        -   /              \
|      /   \/                \
|     /                       \
|    /                ______\
|--/
____________________________________________________

where the black line suddenly shoots back. This can occur either in the 
beginning of the plot (on the left) or at the end. Any ideas what could 
cause this? I assume it's some sort of artifact, right?

Any help is greatly appreciated.

Daniel

___________________________________________

email Daniel.Bozinov at nih.gov