Entering edit mode
9 months ago
Felipe
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0
Hello everyone,
I have several sequences of the whole mitochondrial genome of the Yellow Crazy Ant and I also have (from NCBI: https://www.ncbi.nlm.nih.gov/nuccore/NC_039576.1) the annotation of the genome.
I would like to filter my full sequences to leave only the protein-coding sequences from the 13 genes found in the mitochondria. Can anyone help me, please, on how to do that? I searched for it but couldn't find an answer that fit my situation.
Sorry if it is a very common question here or on Stacks, but I'm very new to this and still getting the hang of it. Thank you very much!
Cheers, Felipe
Why don't you download CDS sequences directly and search for those genes? There is an option on NCBI to export the CDS sequences for a NCBI record OR you can use FTP (GenBank/RefSeq).
Regards,
Nitin N.
Dear Nitin,
thanks for your answer, but sorry, can you be more specific? Are you telling me to download the CDS (which I did now), align it with my sequences, and then manually (for each sequence of mine) delete the bases that are not aligned with the CDS downloaded? That is what I understand.
Thanks again! Regards, Felipe
Hi Nitin, I read your answer again and I think I understand it better now. You might have misunderstood me.
I have sequences of the full mitogenome of this ant species. They are not downloaded from NCBI, I sequenced them. I have the intention to build a phyl. tree with the CDS of the mitogenome of these specimens I collected and sequenced.
What I would like to know is if I can do in an automated way the filtering of the whole sequence to leave only the CDS parts to use. Can you help me, please? Or someone else?
Thank you so much! Felipe
Thank you for the clarification, I thought you downloaded this mitogenome from NCBI. You have provided the link as well.
But now I think I understood your problem. In this situation, I would suggest using some gene prediction tools (Prokka, Prodigal, GeneMark, OR any other you might feel comfortable with) on your mitogenome, this will help you to get the CDS sequences for the predicted genes and then you can proceed with downstream analysis.
Additional Note: There is one webserver called MITOS you can use to annotate your mitogenome.
Regards,
Nitin N.
Thank you so much for your help. I'll proceed with these tools.