How do I make a .rnt file for EDGE-pro. What is it, and can it be made from a .gbk file?

Question

[hr.andreaskjaer]

Hello,

I am working on a transcriptomics experiment. It is for a bacterial genome, that has no .rnt or .ptt file made for it. EDGE-pro which I'm using, requires both of those files. I realized that I could convert a .gbk file to a .ptt file.

Is there a tool to create .rnt files (from .gbk maybe?), or some ingenious script to extract the information from a .gbk file. As I understand, .ptt are protein table files and .rnt is non-coding RNA table files.

Hope you can help!

Andreas

Answer 1

[malteherold]

Hi,

sorry that you had to wait 4 months for an answer..

.rnt files contain RNA features usually rRNA, tRNA

you can write .ptt and .rnt files from a genbank file for example with bioperl:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

and select CDS or RNA features with $feature_object->primary_tag and write entries to the according file.

This might also be helpful: Problem combining ptt, rnt files

However note that you need a .ptt or .rnt file for each replicon e.g. when your bacterial genome consists of multiple contigs or contains plasmids.

I wrote a short script to write .ptt and .rnt files from a gff file but I'm not sure how to upload this here, let me know if I should send it to you.

Best,

Malte

Answer 2

[Ranjit]

check this https://github.com/sgivan/gb2ptt