Hi, I'm new to bioinformatics and I need to compare two bacterial genomes. These genomes come from different strains of the same species. and both genomes are available in NCBI
What I need to do is a genome wide comparison to find the homologous genes in both sequences and what is the name of both locus tags.
In other words I need a table that says Gene A corresponds to Gene B.
I've searched around and found some tools that might help me, for example, microbializer (which is not working) and orthologr but after 10 days of running a power shortage terminated my run and the results I could get were in protein code and not in gene code.
Anyone knows any tool that might help me?
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Andrea Laura •
What about microbializer isn't working? I see their github was updated a year ago. What have you tried to get it working? And what are you running things on? 10 days to compare 2 similar genomes seems excessive.
Other tools you could look at include OrthoMCL and OrthoFinder. That's good for genome-wide analyses as they clusters based on sequence similarity. If you want to be more sure that a transcript/protein is the same in both assemblies you could use a hmm based tool like HMMER.
If you also download an annotation file (GFF/GTF), then you can see what proteins/transcripts are part of which genes and which chromosome/contig they are located on.
As far as I could see microbializer is a web tool and that isn't working. I tried to find how to run it locally and didn't find how to do so. The other program i tried I run it on my personal laptop, thats all i have access to :/
You can use https://github.com/soedinglab/mmseqs2/wiki#reciprocal-best-hit-using-mmseqs-rbh. For two bacterial genomes you can run it easily on a laptop in a matter of minutes. It's basically like blasting genome vs genome and returns the best batch for each feature.
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