Hi Yoram!

Here are some great web tools for comparing your E. coli genomes and identifying differences:

Web-based tools:

• JSpeciesWS (https://jspecies.ribohost.com/jspeciesws/) - Great for ANI calculations and finding genomic divergences
• EzBioCloud ANI (https://www.ezbiocloud.net/tools/ani) - User-friendly, perfect for bacterial strain comparisons
• CoGe (https://genomevolution.org/coge/) - Comprehensive platform with excellent visualization of genomic variations
• Proksee (https://proksee.ca/) - Complete suite that lets you compare multiple genomes visually

Download options:

• Mauve - Excellent for structural rearrangements (simple Java download required)
• MUMmer - Powerful for SNPs and indels (command-line or via Galaxy servers)

For a comprehensive overview of bacterial comparative genomics tools, check out: https://holtlab.net/2015/02/25/tools-for-bacterial-comparative-genomics/

I'd recommend starting with Proksee or CoGe for the best visualization of differences between your strains.

Good luck with your analysis!

Best regards

Thanks Fausto Cabezas-Mera

I did try Proksee, which is indeed a nice visualisation tool, but I didn't find a way to get the differences, and especially genes that exist in one but not the other :-(

What would be ideal is a list of the different sequences, in FASTA or similar format. Maybe I missed something?

If anyone is interested, https://microbializer.tau.ac.il/ seems to do a decent job!

Now I have a clearer picture. I recommend using the Proteome Comparison tool from BV-BRC - it's very good and only requires creating an account and understanding the workflow, which is relatively straightforward. Here are the links:

BV-BRC Proteome Comparison: https://www.bv-brc.org/app/SeqComparison

Manual and Tutorial: https://www.bv-brc.org/docs/quick_references/services/proteome_comparison_service.html

I think this option is the most user-friendly, as other tools like ARTEMIS (https://www.sanger.ac.uk/tool/artemis-comparison-tool-act/), CompareGenome (https://github.com/gmoro-bioecopest/CompareGenome), and even Roary require terminal usage in some cases.

The BV-BRC tool will give you exactly what you're looking for - differential gene lists in downloadable formats, including FASTA files of unique sequences. It's web-based, well-documented, and designed specifically for this type of comparative analysis.

Best regards