Generating a genbank file from a subsection of a larger gbk file - (Jun/05/2008 )
Is there any genome browser that can export a subsection (e.g. 50 kb fragement) of a larger genbank file of a bacterial genome, keep all annotations, but reset the sequence numbering?
Genbank can do this for you. At the bottom of the header are two boxes with a red "begin" and "end" in them. If you change those to numerical coordinates, decide on reverse complement or not, and hit the "refresh" button, it will display the portion you selected with an abbreviated annotation and a re-numbered sequence. You can also click on any mouse sensitive feature in the annotation to select just that portion of sequence.
Thank phage, I neglected to include that this is a genome that has not yet been deposited into genbank, as it has not been published yet. A collaborator is interested in examining certain segments and not the whole genome....Any ideas?