How to extract interoperonic sequences?

Question

[araujopa]

Hello everyone!

I have recently came across something interesting. I need to extract the interOPERONIC (not intergenic) sequences from a genome file (the complete genome, genbank file, etc...). For instance, I have all files (genome, annotation, etc) for Mycobacterium_tuberculosis_H37Rv_uid170532/NC_018143. Then I have this operon file http://genome2d.molgenrug.nl/Bacteria//Mycobacterium_tuberculosis_H37Rv_uid170532/NC_018143.operon

So, before I have to program something I was wondering if Do you guys know any tool that extract the interoperonic sequences based on these data?

Thanks in advance.

Answer 1

[GenoMax]

Since you know the start/stop coordinates you want to extract the sequence for you could do it simply by using Entrez utilities. Here is an example I had posted yesterday: Retrieving batch of selected regions sequences from a NCBI db If you have a large number of these then you may need a script otherwise a series of look-ups should do it.

[araujopa]

Thanks! I will try it!

[araujopa]

Yep. That's pretty much what I needed. I will have to code a little script but nothing major. Thanks!