Question: Discriminating ortholog and paralogs using Cd-hit
0
gravatar for sharmatina189059
8 days ago by
United States
sharmatina18905930 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 • 93 views
ADD COMMENTlink written 8 days ago by sharmatina18905930
1

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 8 days ago by jrj.healey10k

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

ADD REPLYlink written 8 days ago by sharmatina18905930
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1992 users visited in the last hour