CORE genes detection in two closely related species

Question

[Mehmet]

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

Answer 1

[h.mon]

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?

[Mehmet]

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.