Question: Discriminating ortholog and paralogs using Cd-hit
gravatar for sharmatina189059
22 months ago by
United States
sharmatina18905940 wrote:

Dear all I have 40 genomes of bacterial and I need to identify ortholog and paralog genes along with core, dispensable and unique genes. I have used CD hit to make homologous gene clusters and calculate the genes in every cluster. 1- what to do for calculating core gene, accessory genes and unique genes. 2- How can I identify paralogs and orthologs genes? 3. clusters having only representative (*) gene with no alignment (>90% identity) can be considered as unique? Please help.

gene genome • 556 views
ADD COMMENTlink written 22 months ago by sharmatina18905940

What organism are you working with?

CD-HIT alone cannot tell you all of these things. You’d be best off using a pan/core genome pipeline such as roary or OrthoMCL etc.

ADD REPLYlink written 22 months ago by Joe18k

ok.. let me try these tools.. thank you so much

ADD REPLYlink written 22 months ago by sharmatina18905940
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