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Old 11-30-2015, 10:48 AM   #1
aprice67
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Location: New York

Join Date: Nov 2012
Posts: 49
Question Identifying orthologous genes between two bacterial strains

Hi,

I currently am looking at two different strains of the same bacteria. I have RNA-seq data and reference genomes from NCBI. What I want to do is find the following information:
  1. Genes that exist in A, but not in B.
  2. Genes that exist in both A and B. (Including start/end positions)
  3. Genes that do not exist in A, but exist in B.

Very venn diagram sort of stuff here.

I tried making a blast database from A and B, then blasting them against each other, and selecting the set of genes that met criteria like high identity and significant length (over 200), but this way I'm only able to identify 100-200 genes, when there are around 5000 in these genomes.

Can anyone offer some advice or point me toward a tool that will help me accomplish this? Thanks very much in advance.

Last edited by aprice67; 11-30-2015 at 10:51 AM.
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