[Seqinr-forum] Oriloc plot issues

[Jean lobry]

>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
>

Daniel,

my educated guess would be that there is a CDS that wraps around
the genome in you data. A simple fix is to delete the first and
last entries as in :

###
ori <- oriloc()
draw.oriloc(ori[-c(1, nrow(ori)),])
###

or to play with the "rot" argument in oriloc() to make a circular
permutation of the genome so that there is no more CDS wraping around
the genome.

I don't remember if attachments are allowed on this list. There is
a maximum size of 400 K for the text body. I'm trying to attach a
small fasta file here to see what happens.

Best,

-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/
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