Finding marker genes in draft genome

Question

[runnerdaniel]

I have a bacterial draft genome, obtained through metagenomic binning (~400 contigs). I tried to find and extract small ribosomal subunit sequences from the draft genome using phylosift and checkM, which I could use for phylogenetic analysis, however neither software was able to find any. Now I am looking for other possible marker genes in the draft genome, which other marker genes can be suitable? And more importantly I was looking for tools to extract other possible marker genes (not just SSUs), but have not found anything useful. Any suggestions?

I appreciate any help!

Thank you!

Answer 1

[onestop_data]

For future reference, an easy way to find and extract market genomes in a draft genome is using Genome Peek which is a online. All you need to do is to upload the FASTA file for your draft genome. It will classify the taxa on it (which you probably don't care), but will allow you to pull the market geno