[Seqinr-forum] usage of oriloc

[Jean Lobry]

Le 05/06/2014 02:35, Brami, Daniel a écrit :
> Hi Dr. Lobry,
>
> I am trying to use your ‘oriloc’ package on some assembled sequences in
> order to circularize and cut them at their origin of replication.
>
> I came across your package recently and I have been trying to figure out
> how to go from input to desired output but could not find any complete
> examples.
>
> My input would be an assembled scaffold.fasta
>
> My output would be a reordered.scaffold.fasta which begins at the oriC
> and does not truncate any genes given the genome is known to be circular.
>
> Could you offer some help please?
>
> Bien a vous,
>
> Daniel Brami
> Synthetic Genomics, Inc.
> Senior Research Associate, Bioinformatics
> 11149 North Torrey Pines Road
> La Jolla, California  92037
> Phone: 858.433.2230
> Fax: 858.754.2988
> DBrami at SyntheticGenomics.com <mailto:DBrami at SyntheticGenomics.com>
> www.SyntheticGenomics.com <http://www.syntheticgenomics.com/>

Daniel,

oriloc is distributed as a function of the R seqinr package, its
usage is given by entering ?oriloc at your R prompt, also available
online here:

http://www.inside-r.org/packages/cran/seqinr/docs/oriloc

I'm not sure if I understand correctly what you want to do,
I include the seqinr forum discussion list in CC to correct
my assumptions if they are wrong here.

Oriloc works with already assembled sequences in fasta or
GenBank format. Usually complete genomes are taken as input
but using a partial one is possible. I'm unsure that your
are exactly in this situation.

Best,

JLO