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CORE genes detection in two closely related species

Dear all,

I have two closely related species (A and B) in the same genus. They are worms. I have assembled genomes of these two species. I made blast database on unix using 248 CORE genes (protein sequences) from CEGMA website. I have a protein fasta file of species A. My questions are:

  1. Should I find first a core gene in genome A, then find the same core gene in genome B
  2. Or should I find a core gene in genome A , and then Should I find the gene in the genome A which is close to the core gene in genome B?
  3. How to find nucleotide sequence of core genes in genome files?
  4. How to convert DNA sequence of a genome file into protein sequence?

Thanks

alignment genome gene
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updated by Ram Ram • written by Mehmet Mehmet

1 answer

1. yes, find the core genes in both genomes, then compare lists - consider the core as a "gold standard" to which your drafts should be compared.

2. no, not for finding core genes common to both - if drafts are fragmented, you may miss genes which are actually present in both.

3. if you are running CEGMA, I believe this is part of the output.

4. you said you already have a protein fasta. How did you obtain it?

• 0 views • link
written by h.mon h.mon

I have run CEGMA for two species. yes I have a protein fasta file given by my supervisor. I don't know how to convert a genome DNA sequence file into protein file.

Thank you for your help.

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written by Mehmet Mehmet

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