Answers.Body: <p>The only way I can think is to break the protein apart on methionine residues, blast each amino acid locus and concatenate any locus that does not score a query protein position of '1'. The theory is simple every protein starts with a methionine residue, however there are plenty of M residues within the protein that don't represent the beginning of the gene.</p>
  
  <p>Breaking the protein apart on M would be easy, but then automating and parsing the blast would be fiddly. Obvioulsy you will need to code it and if its a one off would it be worth it?</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-13T04:33:44.560Z
Answers.LastActivityDate: 2020-03-13T04:33:44.560Z
Answers.UserDisplayName: M__
Body: <p>I have a 120-concatenated protein sequence in a fasta file. I would like to split by proteins.
  How can I identify each protein?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-09T16:08:11.003Z
Comments.Text: Do you have a multi-fasta file (A FASTA file with multiple sequences, each with its own header) or a mangled FASTA file with one sequence that is in reality 120 individual sequences concatenated?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-09T16:17:13.040Z
Comments.Text: A FASTA file with only one sequence.
Comments.UserDisplayName: Manolo Dominguez Becerra
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-09T16:21:07.833Z
Comments.Text: In that case, how do you determine where one protein ends and another begins? How was this file generated?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-09T16:33:12.897Z
Comments.Text: That is what I want to know. The file was generated using GTDBtk, a toolkit programme that identifies 120 genes marker to perform taxonomic classifications. I am using this programme for another purpose. I need the sequence of each protein, but I am afraid I am not going to be able to do it, right?
Comments.UserDisplayName: Manolo Dominguez Becerra
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-09T16:51:57.277Z
Comments.Text: sounds really tough unless you know how it was joined in the first place
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-09T17:00:21.520Z
Comments.Text: Rerun GTDBtk so that it does not output all protein sequences into a single fasta file. I am not sure what is the correct usage for it, but typical bioinformatics software should not do it by default. Alternatively, look for non-amino acids characters in the output as possible delimiters. Or perhaps these are subsequences of fixed length, rather than entire proteins, in which cases split the sequence into 120 equal length substrings.
Comments.UserDisplayName: Timur Shtatland
Tags: <phylogenetics><fasta><proteins>
Title: Identifying proteins in a concatenated protein sequences
ThreadText: # Identifying proteins in a concatenated protein sequences
  
  (Asked by: username_0 on 2020-03-09)
  
  I have a 120-concatenated protein sequence in a fasta file. I would like to split by proteins.
  How can I identify each protein?
  
  **Tags:** phylogenetics, fasta, proteins
  
  > **Comments:**
  > **username_1**: Do you have a multi-fasta file (A FASTA file with multiple sequences, each with its own header) or a mangled FASTA file with one sequence that is in reality 120 individual sequences concatenated?  
  > **username_0**: A FASTA file with only one sequence.  
  > **username_1**: In that case, how do you determine where one protein ends and another begins? How was this file generated?  
  > **username_0**: That is what I want to know. The file was generated using GTDBtk, a toolkit programme that identifies 120 genes marker to perform taxonomic classifications. I am using this programme for another purpose. I need the sequence of each protein, but I am afraid I am not going to be able to do it, right?  
  > **username_2**: sounds really tough unless you know how it was joined in the first place  
  > **username_3**: Rerun GTDBtk so that it does not output all protein sequences into a single fasta file. I am not sure what is the correct usage for it, but typical bioinformatics software should not do it by default. Alternatively, look for non-amino acids characters in the output as possible delimiters. Or perhaps these are subsequences of fixed length, rather than entire proteins, in which cases split the sequence into 120 equal length substrings.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2020-03-13. Score: 1
  
  The only way I can think is to break the protein apart on methionine residues, blast each amino acid locus and concatenate any locus that does not score a query protein position of '1'. The theory is simple every protein starts with a methionine residue, however there are plenty of M residues within the protein that don't represent the beginning of the gene.
  
  Breaking the protein apart on M would be easy, but then automating and parsing the blast would be fiddly. Obvioulsy you will need to code it and if its a one off would it be worth it?
  
  
  ---
  
  