Body: <p>I have an aligned metagenome fasta file. I want to see the relation between the aligned genes and the so-called Clusters of Orthologous Groups (<a href="https://www.ncbi.nlm.nih.gov/research/cog-project/" rel="nofollow noreferrer">COGs</a>). For the purpose of the analysis I am using the <a href="https://github.com/songweizhi/BioSAK/blob/master/doc/COG2020_cn.md" rel="nofollow noreferrer">BioSAK COG2020 CLI</a> but it looks like I have to align my DNA sequences differently and not by genes. Does somebody know how the sequences should be aligned for the CLI to produce meaningful results? The results set of COGs is empty. The problem is that these are nucleotide gene annotations from the Silva database. I suppose BioSAK expects annotated protein sequences but I have Nucleotide annotated sequences. The main question is: Is it possible to translate the Nucleotide to Protein sequences and annotate them to be used with BioSAK and do you know of a pipeline that does that?</p>
  <p>Example command:</p>
  <pre><code>BioSAK COG2020 -m N -t 6 -db_dir ./COG_db_dir -i input.ffn
  </code></pre>
  <p>Example input Nucleotide fasta format:</p>
  <pre><code>&gt;AB679109.1
  GTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAA
  AGCGCGCGCAGGCGGATCAGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATG
  GGATGGAAACTGCTGATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGT
  GAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACT
  GACGCTGAGGCGCGAAAGCCAGGGGAGCGAACGGGATTAGAAACCCCAGTAGTCC
  </code></pre>
  <p>Example from the COGs 20 fasta database:</p>
  <pre><code>&gt;AAM04025_1 glutamate-1-semialdehyde 2,1-aminomutase [Methanosarcina acetivorans C2A]
  MVSEVTLDKSRQMYEKAKTLIPGGVSSPVRAIKPYPFYTASADGSKIRDLDGNEYIDYCLAYGPAVLGHNHPVIKAAIKEQLDKGWLYGTPTELEVTLAEKVAGYYPSIDMLRFVSTGTEATMSALRLARGFTRKNKFIKIEGGFHGAHDAVLVKAGSGATTLGEPDSLGIPADFTKYTLQAPYNDIETMTTLVEKNRDDLAAVIIEPVLGNIGPILPLPGYLKELRKLTKENDVLLIFDEVITGFRLAMGGAQEYFGVVPDMTTLGKIVGGGLPIGVFGGRREIMEMIAPSGAVYQAGTFSGSPCSVAAGIAVLDYLKKEDIHAKLNSTGDYMRAVVSEIVEDEGLDYTVCGIASMFKIFFGAEPHNYQEALKCDKEGYLSFFHRMLANGVFLPPSQFETNFISAAHSEEDIEKTLEAYVENL
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-11-14T12:25:58.840Z
Comments.Text: Please [edit] your question and give us a bit more detail. What is wrong with the output you are getting now? Do you get some sort of error message? What is it? Can you give us an example of you actual input (that's just a single fasta sequence, not an aligned file where we would need at least two). What exactly is your "aligned metagenome" file? What is it aligned against? Have you grouped by genes and aligned each gene? How did you identify the genes? Are they annotated or did you predict them? Are these bacteria?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-11-15T05:15:05.473Z
Comments.Text: Please show the first few lines of the results you're getting with your examples.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-11-23T08:33:15.357Z
Comments.Text: I have edited my question with more descriptive questions and info. The main question is can I extract COGs from Nucleotide-annotated sequences without additional protein sequencing?
Comments.UserDisplayName: Ivan Ugrin
Tags: <phylogenetics><gene>
Title: Metabolite function from DNA sequences
ThreadText: # Metabolite function from DNA sequences
  
  (Asked by: username_0 on 2024-11-14)
  
  I have an aligned metagenome fasta file. I want to see the relation between the aligned genes and the so-called Clusters of Orthologous Groups ([COGs](https://www.ncbi.nlm.nih.gov/research/cog-project/)). For the purpose of the analysis I am using the [BioSAK COG2020 CLI](https://github.com/songweizhi/BioSAK/blob/master/doc/COG2020_cn.md) but it looks like I have to align my DNA sequences differently and not by genes. Does somebody know how the sequences should be aligned for the CLI to produce meaningful results? The results set of COGs is empty. The problem is that these are nucleotide gene annotations from the Silva database. I suppose BioSAK expects annotated protein sequences but I have Nucleotide annotated sequences. The main question is: Is it possible to translate the Nucleotide to Protein sequences and annotate them to be used with BioSAK and do you know of a pipeline that does that?
  
  Example command:
  
  ```
  BioSAK COG2020 -m N -t 6 -db_dir ./COG_db_dir -i input.ffn
  
  ```
  
  Example input Nucleotide fasta format:
  
  ```
  >AB679109.1
  GTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAA
  AGCGCGCGCAGGCGGATCAGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATG
  GGATGGAAACTGCTGATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGT
  GAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACT
  GACGCTGAGGCGCGAAAGCCAGGGGAGCGAACGGGATTAGAAACCCCAGTAGTCC
  
  ```
  
  Example from the COGs 20 fasta database:
  
  ```
  >AAM04025_1 glutamate-1-semialdehyde 2,1-aminomutase [Methanosarcina acetivorans C2A]
  MVSEVTLDKSRQMYEKAKTLIPGGVSSPVRAIKPYPFYTASADGSKIRDLDGNEYIDYCLAYGPAVLGHNHPVIKAAIKEQLDKGWLYGTPTELEVTLAEKVAGYYPSIDMLRFVSTGTEATMSALRLARGFTRKNKFIKIEGGFHGAHDAVLVKAGSGATTLGEPDSLGIPADFTKYTLQAPYNDIETMTTLVEKNRDDLAAVIIEPVLGNIGPILPLPGYLKELRKLTKENDVLLIFDEVITGFRLAMGGAQEYFGVVPDMTTLGKIVGGGLPIGVFGGRREIMEMIAPSGAVYQAGTFSGSPCSVAAGIAVLDYLKKEDIHAKLNSTGDYMRAVVSEIVEDEGLDYTVCGIASMFKIFFGAEPHNYQEALKCDKEGYLSFFHRMLANGVFLPPSQFETNFISAAHSEEDIEKTLEAYVENL
  
  ```
  
  **Tags:** phylogenetics, gene
  
  > **Comments:**
  > **username_1**: Please [edit] your question and give us a bit more detail. What is wrong with the output you are getting now? Do you get some sort of error message? What is it? Can you give us an example of you actual input (that's just a single fasta sequence, not an aligned file where we would need at least two). What exactly is your "aligned metagenome" file? What is it aligned against? Have you grouped by genes and aligned each gene? How did you identify the genes? Are they annotated or did you predict them? Are these bacteria?  
  > **username_2**: Please show the first few lines of the results you're getting with your examples.  
  > **username_0**: I have edited my question with more descriptive questions and info. The main question is can I extract COGs from Nucleotide-annotated sequences without additional protein sequencing?  
  
  ---
  
  ## 0 answers
  
  