[EMBOSS] Restriction fragment sequences

[Peter Rice]

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).

With the command line option -rformat listfile you can then use seqret to return 
the sequences but using @filename as input.

Unfortunately if you do that with restrict you only get the restriction sites.

We will add a new application to the next release.

regards,

Peter Rice