Answers.Body: <p>I am having a very similar issue, however mine are multiple sequences of the same specie. I have a mixture of DNA and RNA sequences so although it appears to aligning fine the proteins produced are not correct. I’m at a loss on how to fix this so if you managed to figure out what to do please let me know.</p>
  
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Answers.Text: Please submit this as a separate question.
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Body: <p>I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding genes, every fasta file includes genes from many species that are orthologs/paralogs. These genes even in the same species may use different genetic codes. My goal is to align the sequences, codon alignment [the process of codon alignment considers the reading frame of the translated protein and adjusts the nucleotide alignment so that the protein alignment stays in frame.] , and afterwards to create N-J trees. For the whole process I work on MEGA11. I cannot organize the species-genes into groups with common genetic codes because I need all of them in the tree. One option, to my mind at least, would be the alignment not in codon but in DNA,or another option is to align their protein sequences or lastly a third option could be the change of the sequences in order to get rid of the stop codons and afterwards to use one common code for everything, by doing that I know that I will lose some info but at least I can work.Do you have any idea how to overcome this obstacle? Do you agree with any of this options? Thank you in advance!</p>
  
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Comments.CreationDate: 2023-12-06T05:20:26.217Z
Comments.Text: Can you say a little more about how diverse the organisms that you're studying are? Hominins? Carnivores? Mammals? Vertebrates? Eumetazoa? Eukarya? Scale matters! the more distantly related your organisms are (including divergent genetic codes), the more you would want to use a more stable data type such as protein sequence.
Comments.UserDisplayName: Maximilian Press
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Comments.Text: Why is the genetic code relevant? There are not that many genetic codes out there, and most differences are around stop codons as you point out, but if you are aligning nucleotides, it shouldn't really matter. What does "not in codon but in DNA" mean? And yes, aligning proteins would make sense, did you try that?
Comments.UserDisplayName: terdon
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Comments.Text: I though the main differences were the relative abundancies of different codon triplets for the same aa i think they call it codon usage
Comments.UserDisplayName: pippo1980
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Comments.Text: @pippo1980 no, that's a different thing. There are a few different genetic codes used by some species, and even our own mitochondria. See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2.
Comments.UserDisplayName: terdon
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Comments.Text: Cool , how they were able to identify them ? From genetic analysis or native protein sequencing , maybe by mass spec ? Or trna and synthases study ??
Comments.UserDisplayName: pippo1980
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Comments.Text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8629427/#:~:text=The%20first%20alternative%20genetic%20codes,obtained%20by%20direct%20protein%20sequencing. A computational screen for alternative genetic codes in over 250,000 genomes , here I got some background info, thanks @terdon
Comments.UserDisplayName: pippo1980
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Comments.Text: Its probably easy but want to avoid an explaination because as other site members point out the question lacks key details and there's risk of a "thats not what I meant" response.
Comments.UserDisplayName: M__
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Comments.Text: @MaximilianPress I am working with every species listed on the Plants, Protists and Fungi subcategories mentioned here https://www.genome.jp/kegg/catalog/org_list.html ,these are the organims that KEGG database has.
Comments.UserDisplayName: George X.
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Comments.Text: @pippo1980  To give a better picture of my project I am working on paralog genes as they are mentioned on KEGG, there is a specific option for that on KEGGs website. After I download the sequences I align them on MEGA11 and I create N-J trees. Every tree constits of genes (paralogs+orthologs) that belong on the same KO (ortholog code). My rpoblem is that many of these paralog genes are found on different positions (mitoch. or nucleus) so I cannot align them as codons because in most cases they use differerent genetic code. My question is how can I overcome this difficulty.
Comments.UserDisplayName: George X.
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Comments.Text: @terdon I am working with gene coding sequences, do you think that if I align them as non-coding sequences there would be a major diffenence in my alignment? By "not in codon but in DNA" I mean what exactly I just wrote down here, I mentioned it like that because this is how it is mentioned on the MEGA11 program. Here I give you an example of 2 paralog genes that are located on differnent positions (mitoch. and nucleus), this in not a rare ocassion for my dataset. https://www.genome.jp/entry/taes:123096964 https://www.genome.jp/entry/taes:34688768
Comments.UserDisplayName: George X.
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Comments.CreationDate: 2023-12-12T04:53:47.863Z
Comments.Text: My sense is that you are overthinking it- just use protein sequence!
Comments.UserDisplayName: Maximilian Press
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Comments.CreationDate: 2023-12-12T17:46:52.680Z
Comments.Text: Any codon alignment tool that remove this genetic code differences , keep in mind I dont know about how much different they could be, like sterilizes the codon differences removing them from the scores or treat them as identical ? Not sure this make any sense but maybe ....
Comments.UserDisplayName: pippo1980
Tags: <phylogenetics><multiple-sequence-alignment><codon><megax>
Title: Aligning sequences with multiple genetic codes!
ThreadText: # Aligning sequences with multiple genetic codes!
  
  (Asked by: username_0 on 2023-12-06)
  
  I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding genes, every fasta file includes genes from many species that are orthologs/paralogs. These genes even in the same species may use different genetic codes. My goal is to align the sequences, codon alignment [the process of codon alignment considers the reading frame of the translated protein and adjusts the nucleotide alignment so that the protein alignment stays in frame.] , and afterwards to create N-J trees. For the whole process I work on MEGA11. I cannot organize the species-genes into groups with common genetic codes because I need all of them in the tree. One option, to my mind at least, would be the alignment not in codon but in DNA,or another option is to align their protein sequences or lastly a third option could be the change of the sequences in order to get rid of the stop codons and afterwards to use one common code for everything, by doing that I know that I will lose some info but at least I can work.Do you have any idea how to overcome this obstacle? Do you agree with any of this options? Thank you in advance!
  
  **Tags:** phylogenetics, multiple-sequence-alignment, codon, megax
  
  > **Comments:**
  > **username_1**: Can you say a little more about how diverse the organisms that you're studying are? Hominins? Carnivores? Mammals? Vertebrates? Eumetazoa? Eukarya? Scale matters! the more distantly related your organisms are (including divergent genetic codes), the more you would want to use a more stable data type such as protein sequence.  
  > **username_2**: Why is the genetic code relevant? There are not that many genetic codes out there, and most differences are around stop codons as you point out, but if you are aligning nucleotides, it shouldn't really matter. What does "not in codon but in DNA" mean? And yes, aligning proteins would make sense, did you try that?  
  > **username_3**: I though the main differences were the relative abundancies of different codon triplets for the same aa i think they call it codon usage  
  > **username_2**: @username_3 no, that's a different thing. There are a few different genetic codes used by some species, and even our own mitochondria. See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2.  
  > **username_3**: Cool , how they were able to identify them ? From genetic analysis or native protein sequencing , maybe by mass spec ? Or trna and synthases study ??  
  > **username_3**: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8629427/#:~:text=The%20first%20alternative%20genetic%20codes,obtained%20by%20direct%20protein%20sequencing. A computational screen for alternative genetic codes in over 250,000 genomes , here I got some background info, thanks @username_2  
  > **username_4**: Its probably easy but want to avoid an explaination because as other site members point out the question lacks key details and there's risk of a "thats not what I meant" response.  
  > **username_0**: @username_1 I am working with every species listed on the Plants, Protists and Fungi subcategories mentioned here https://www.genome.jp/kegg/catalog/org_list.html ,these are the organims that KEGG database has.  
  > **username_0**: @username_3  To give a better picture of my project I am working on paralog genes as they are mentioned on KEGG, there is a specific option for that on KEGGs website. After I download the sequences I align them on MEGA11 and I create N-J trees. Every tree constits of genes (paralogs+orthologs) that belong on the same KO (ortholog code). My rpoblem is that many of these paralog genes are found on different positions (mitoch. or nucleus) so I cannot align them as codons because in most cases they use differerent genetic code. My question is how can I overcome this difficulty.  
  > **username_0**: @username_2 I am working with gene coding sequences, do you think that if I align them as non-coding sequences there would be a major diffenence in my alignment? By "not in codon but in DNA" I mean what exactly I just wrote down here, I mentioned it like that because this is how it is mentioned on the MEGA11 program. Here I give you an example of 2 paralog genes that are located on differnent positions (mitoch. and nucleus), this in not a rare ocassion for my dataset. https://www.genome.jp/entry/taes:123096964 https://www.genome.jp/entry/taes:34688768  
  > **username_1**: My sense is that you are overthinking it- just use protein sequence!  
  > **username_3**: Any codon alignment tool that remove this genetic code differences , keep in mind I dont know about how much different they could be, like sterilizes the codon differences removing them from the scores or treat them as identical ? Not sure this make any sense but maybe ....  
  
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  ## 1 answers
  
  ### Answer by username_5 on 2024-01-25. Score: 0
  
  I am having a very similar issue, however mine are multiple sequences of the same specie. I have a mixture of DNA and RNA sequences so although it appears to aligning fine the proteins produced are not correct. I’m at a loss on how to fix this so if you managed to figure out what to do please let me know.
  
  > **Comments:**
  > **username_6**: Please submit this as a separate question.  
  
  ---
  
  