How can I discover gene function on a bacterial genome

Question

[vicslab]

I have a bacterial genome, but I need more information about it.

I have made Roary to have the clusters of orthologous genes, like OrthoMLC does. I would like to know what softwares I can use to discover the biological function of these genes. I want to split these groups into their functions to have a better understanding.

[Asaf]

You can use eggNOG-mapper

[Fatima]

https://sourceforge.net/projects/fun4me/ This package might help.

[mail2steff]

You can also check https://github.com/robotoD/GenoVi

Answer 1

[h.mon]

Prokka is a very fast and efficient bacterial genome annotation pipeline. You can install it with conda and run locally the annotation.

RAST is an annotation server, in addition to a good annotation, it also provides lots of summaries and figures about the annotation. There is a waiting line, but it shouldn't take longer than a day do finish one genome.

Answer 2

[onestop_data]

Prokka can be complicated to install because of tbl2asn dependency. I show as part of this tutorial on how you can use it step-by-step .

[Asaf]

The fix might be really around the corner, since tbl2asn-forever hack is now on bioconda: https://anaconda.org/bioconda/tbl2asn-forever

[onestop_data]

Thanks. I saw the tweet, but I was not aware it was on conda already.

[onestop_data]

I have updated the blog post.