Question: Which tools for the analysis of the evolution of bacterial genomes ?
gravatar for quentin.lamybesnier
2.8 years ago by
quentin.lamybesnier0 wrote:

Hello everyone,

I am currently working on the data of bacteria that have been moved from an environment to another, and then sequenced frequently. I am therefore looking at any tools that I could use to get data on the evolution of my functionnal genomes, as I am relatively inexperienced in bioinformatics. So far, I already looked at prophages and mobile elements. For example, if I could have for each genome a quantification of each GO category of my genome, then I could see what GO terms have progressed and regressed over time, but I didn't manage to find tools to do that easily. I'll take any piece of advice !

Thank you in advance,


ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 2.8 years ago by quentin.lamybesnier0

Mauve should be on your list of things to check. It will help you align the genomes and figure out the changes.

ADD REPLYlink written 2.8 years ago by genomax62k

Thank you for your answer. Unfortunately, my data is limited to contigs file, so I can't actually make any sort of alignment of the genomes.

ADD REPLYlink written 2.8 years ago by quentin.lamybesnier0

Sounds like this is more than one bacterium is in the mix. You are going to have a difficult time tracking changes over time (unless it is a known number of species in the mix and your sampling works well along with your ability to bin the reads to correct genomes). Short reads are tough to uniquely assign if the species are related and/or you have a multi-mapping situation.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax62k

I have 1 fasta file for each year, and it is always the same bacterium. However it is possible that all the strains extracted are not clonal. It is really because of the contigs nature of my data that I can't align them. My problem is that regular annotation methods (I used prokka) produce a lot of data in a very qualitative way, and there's no way for me to easily compare the strains out of those results. What I'd like is a tool that could produce a summary of the genome's functionnal information in a quantitative way. Then I could tell what functions were lost the most in my genomes or such things.

ADD REPLYlink written 2.8 years ago by quentin.lamybesnier0
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