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!
1 answer
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
At least two of them are automatic: Roary and BPGA.
Both of them are based on OrthoMCL-ortholog rearch program.
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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.