Creating a 'subsetted' genbank of an operon from a whole genome

Question

[Joe]

First post on biostars, though I play around with phylogenies and assembly/annotation from time to time. I'm by no means an expert (and first and foremost an experimental biologist, not a bioinformatician!) but I suspect this is a pretty simple question to which I can't find an easy answer.

Basically, I have a whole library of annotated GFF files that I made a while back, and I now want to extract some operons from the GFF in to their own files, carrying with them their annotations.

I can use the Sanger Centre's Artemis to easily create a genbank of the highlighted DNA sequence, however it only exports the sequence and none of the annotations.

Is there any way to simply take a selected expanse of DNA (in this case an operon) and create it's own fully-fledged genbank with annotations etc. - or - can I take my 'plain' genbank and feed in annotations from an existing one somehow?

Answer 1

[samuelmiver]

Try with this:

http://www.clcbio.com/products/clc-main-workbench/

CLC is a powerful in order to visualize genomes with annotations. In addition it allows you to generate a genbank only with those features you want to keep (your operon for example).

[Joe]

This seems to do it, thanks - luckily we have it on our server already. One more really daft little question if I may, how can I highlight the first and last genes of the operon, and have CLC highlight everything inbetween? In SnapGene this can be achieved by simply holding shift, and clicking the first and last genes, but CLC doesn't appear to have this option - or is using a different key?

[samuelmiver]

You can select multiple sequence regions using the control key but I am not sure if this is what you need.

P.S. Remember to upvote when you get a good/useful answer in order to help people with same problem find the best solution.

[Joe]

I think I tried control, and it didnt seem to work, though there could have been some confusion as I was using CLC on a Ubuntu machine via X11 and command/control key combos seem to be temperamental.

Answer 2

[Joe]

Did end up writing my own script to do this.

See: A: Script/Application to create a genbank format sub-sequence

Answer 3

[Charles Plessy]

Not sure but would EMBOSS's extractfeat command do what you want ?

[Joe]

Only skimmed it very briefly but I would say not. What I wanted (and ended up coding) was the ability to simple specify a start and end base index and grab everything inbetween as a genbank (to preserve annotations/locustags and so on).

Extractfeat looks like it just allows you to pull out specific features - unless I've glossed over something.

[Charles Plessy]

Indeed, sorry for my misunderstanding.