Annotating Core and Pan genome

Question

[utkarsh.sood]

Hello,

I have used get_homologues pipeline to predict core and pan genome among a group of bacteria. What will be the best method to annotate around 5000 core genes and 9000 pan genes quickly and efficiently?

Thanks!

[GenoMax]

It always helps to do a search on biostars (via your favorite search engine) before asking a new question. There are plenty of threads on this topic (some of which @natasha has linked below) but can also be seen in the "Similar posts" column on the right.

Answer 1

[natasha.sernova]

There are many different tools.

Annotation:

http://geneontology.org/page/annotation-tools-downloads-and-beyond

http://go.princeton.edu/ - also gene ontology

https://omictools.com/genome-annotation-category

There are many relatively recent tools in biostars.org to determine core-genes and pangenomes.

Pan- and core- genome in bacteria

pipelines for pan-genome analysis

A: Pan and core genome analysis

BPGA - Bacterial Pan Genome Analyis pipeline

Roary pan genome analysis: where can I find 'clustered_proteins' for the command Roary query_pan_genome -a union -g clustered_proteins *.gff

At least two of them are automatic: Roary and BPGA.

Both of them are based on OrthoMCL-ortholog rearch program.