[EMBOSS] cirdna

[Jon Ison]

Hi Ryan

So far as I'm aware there are no apps to generate a cirdna input
file, at least not directly.

cirdna has a generic concept of the markers which it displays: a
marker is typically a gene but could be any genetic feature with
a defined range in the sequence.  So it depends on what you want to
show.

If you want to display restriction sites,you could use e.g. restrict
or restover to identify the sites, then convert the appropriate parts
of the output into a format suitable for cirdna.  You'd need to check
the input and output formats from the documentation closely:

http://emboss.sourceforge.net/apps/cirdna.html
http://emboss.sourceforge.net/apps/restrict.html

I don't think there are tools in EMBOSS to do that conversion for
you at the moment.  restrict can generate output as a report format
but cirdna can't currently read a report format.   That could change
though.  If you let us know exactly what you need we can do something
for a future release.

Cheers

Jon




> Two questions:
>
> Is there a program in EMBOSS to generate an input file for cirdna?
>
> Is there a program in EMBOSS to draw a circular piece of DNA and all the
> restriction sites on that piece of DNA?  GCG has a tool to do this, and
> the closest I see in EMBOSS is cirdna.  With GCG, you were able to just
> supply the DNA sequence and it would do the rest.  That doesn't seem to
> be the case here, or am I missing something?
>
> Ryan
>
> --
> Ryan Golhar  -  golharam at umdnj.edu
> The Informatics Institute of UMDNJ
>
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