[EMBOSS] Antwort: Re: Restriction fragment sequences

[David.Bauer at SCHERING.DE]

Hello Peter,

emboss-bounces at lists.open-bio.org schrieb am 02/02/2007 12:28:55:

> Jean-Christophe AME wrote:
> > Hello,
> >
> > I have a question concerning DNA restriction fragment analysis : Is
> > there a way to generate the actual sequence of the restriction
> > fragment generated by restrict or remap, this is to facilitate the in
> > silico construction of recombinant plasmid just with a cut and paste.
> > May there are some ways do this automatically (there was CloneIt but
> > it doesn't work).
>
> Interesting suggestion. You really need a nucleotide version of digest
(or
> restrict with the fragment start/end and sizes reported instead of
> the cut sites).

It would be really good to have this functionality in EMBOSS.
But I guess we need more than just the fragments here.
If we want to ligate a fragment into a vector, than we need also somewhere
the information about the restriction sites at the ends (blunt,
5'overhang, 3'overhang).
So I could imagine to have two applications.
One which is able to create fragments and a description file with
information about the fragments and theire ends. Or maybe one could put
this information in the fasta description line of the created fragment.
And a secon application which would allow to select particular fragments
(from the description file) and than in-silico ligate the fragments.
Optionally it should allow end modifications like Klenow fill-in. So this
application would not just concatenate the fragments but simulate the
ligation reaction.


Cheers,
David.