Good morning
Currently I'm doing a study for bacteriocin gene clusters in bacteria genomes, does anyone knows if I should choose BAGEL3 (maybe BAGEL4) or antiSMASH?
I know that antiSMASH is more general (including NRPS and PKS genes), but for working experience is there any difference with BAGEL3/4?
Please consult the following papers:
Article A large scale prediction of bacteriocin gene blocks suggests...
Article In silico identification of bacteriocin gene clusters in the...
https://academic.oup.com/nar/article/38/suppl_2/W647/1103508
https://www.frontiersin.org/articles/10.3389/fmicb.2017.00876/full
This seems to be pretty late. But there is a new software called NeuBI based on neural networks for predicting bacteriocins. We show that it performs better than the currently existing softwares. You can download it from here-
https://github.com/nafizh/NeuBI
The relevant paper is accepted at Bioinformatics and will soon be out. You can find the pre-print here:
https://www.biorxiv.org/content/early/2018/06/17/255505
Disclosure: I am the author of the software.
Edit: The paper is now out in Bioinformatics.
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty937/5172364?rss=1
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