Hello Peter, [EMAIL PROTECTED] 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. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
