sync prodigal output to Artemis (& to obtain protein identities)

[Rosary Lim]

Hi everyone, I've just tried out the installed version of Prodigal and it did provide outputs for me - 1. CDS 2. Protein translations (without identified names)

I was wondering if anyone here knows of how to channel these Prodigal outputs into Artemis such that I can get some visualizations to make sense out of my results?

And also, it would be great if anyone knows of tool(s) to obtain protein identities/IDs for the translations I obtained?

Kind regards & many thanks,
Rosary

[Torsten Seemann]

Rosary,

Hi everyone, I've just tried out the installed version of Prodigal and it did provide outputs for me - 1. CDS 2. Protein translations (without identified names)
I was wondering if anyone here knows of how to channel these Prodigal outputs into Artemis such that I can get some visualizations to make sense out of my results?
And also, it would be great if anyone knows of tool(s) to obtain protein identities/IDs for the translations I obtained?

My software Prokka uses Prodigal as part of a gene annotation pipeline:

http://www.vicbioinformatics.com/software.prokka.shtml 

It produces a clean .gbk or .gff file that Artemis can load.

If you have trouble installing it, we are working on a web server version, which I may be able to give you beta access too.

--
--Dr Torsten Seemann
--Scientific Director : Victorian Bioinformatics Consortium, Monash University, AUSTRALIA

--Senior Researcher : VLSCI Life Sciences Computation Centre, Parkville, AUSTRALIA
--http://www.bioinformatics.net.au/