Any software/s to find unique genes while comparing genome annotations?

Yes, there are several software tools available that can help you analyze and compare genome annotations to identify unique genes or proteins in your sample. Here are a few commonly used ones:

OrthoFinder: OrthoFinder is a popular software for comparative genomics that can identify orthologous gene groups across multiple genomes. It can help you identify unique genes by comparing the gene content of your annotated genome with a reference genome or multiple genomes.

BLAST (Basic Local Alignment Search Tool): BLAST is a widely used tool for sequence similarity searching. You can use it to compare your annotated gene sequences against a reference genome or protein database to identify unique genes or proteins with significant differences.

Artemis Comparison Tool (ACT): ACT is a genome comparison and visualization tool that allows you to align and compare two or more annotated genomes. It can help you identify unique genes by visualizing the differences between your annotated genome and the reference genome.

Gepard: Gepard is a tool for the visualization and analysis of long nucleotide sequences, including whole genomes. It can be used to identify unique genes or genomic regions by aligning and comparing your annotated genome with the reference genome.

OrthoMCL: OrthoMCL is another tool for orthologous gene clustering and comparative genomics analysis. It can identify unique genes by comparing the gene families or clusters in your annotated genome with those in the reference genome.

These software tools can automate the process of comparing genome annotations and help you identify unique genes or proteins in your sample. Remember to choose the tool that best suits your specific requirements and analyze the results in conjunction with other relevant information to validate any findings.

Ryan Gourlie

To add on Susantas response, there are pangenome tools for comparing many isolates at once such as PanOCT. These will group genes into core and accessory genes. If you want to narrow accessory genes into singletons (present only in a single individual genome) after creating pangenome I have a script that does this. You can get some methods from our recent paper and link to github with some scripts Article The pangenome of the wheat pathogen Pyrenophora tritici-repe...

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