Body: <p>I have a set of population sequence files that I've already aligned, identifying all existing SNVs (A, C, T, G, del) within each population, while excluding inserts and non-singular deletions.</p>
  <p>I now want to translate each aligned sequence and the reference genome into amino acids to detect single amino acid variations.</p>
  <p>Read length is about 100bp.</p>
  <p>What's the best method to achieve this? My current idea is to brute-force translate each aligned sequence inside the mpileup, and the reference genome after alignment, but I'm concerned this might not be the most efficient approach.</p>
  <p>I've heard that UGENE might be capable of handling this task, but I haven't been able to figure out how to use it for this purpose yet. Any advice or alternative suggestions?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-29T23:05:39.100Z
Comments.Text: How large are the sequence files - what is the average individual sequence length and total number of sequences?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-30T06:31:33.357Z
Comments.Text: Read length is about 100bp. Wait i need to check the rest. Why is this relevant?
Comments.UserDisplayName: gl00ten
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-30T10:20:06.733Z
Comments.Text: There are easy ways to do a translation on a small number of sequences; it helps to get an idea of scale to gauge what the best approach is. Running an accurate translation on a few sequences is quite different from running a rough translation on millions of sequences.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-31T00:31:46.840Z
Comments.Text: And what species is this for? Does it have introns and splicing? If so, have you targeted the exons in your sequencing or do those need to be annotated and not translated?
Comments.UserDisplayName: terdon
Tags: <snp><mpileup><snv><amino-acids>
Title: Best Approach for Translating Aligned Population Sequences to Detect Single Amino Acid Variations?
ThreadText: # Best Approach for Translating Aligned Population Sequences to Detect Single Amino Acid Variations?
  
  (Asked by: username_0 on 2024-08-29)
  
  I have a set of population sequence files that I've already aligned, identifying all existing SNVs (A, C, T, G, del) within each population, while excluding inserts and non-singular deletions.
  
  I now want to translate each aligned sequence and the reference genome into amino acids to detect single amino acid variations.
  
  Read length is about 100bp.
  
  What's the best method to achieve this? My current idea is to brute-force translate each aligned sequence inside the mpileup, and the reference genome after alignment, but I'm concerned this might not be the most efficient approach.
  
  I've heard that UGENE might be capable of handling this task, but I haven't been able to figure out how to use it for this purpose yet. Any advice or alternative suggestions?
  
  **Tags:** snp, mpileup, snv, amino-acids
  
  > **Comments:**
  > **username_1**: How large are the sequence files - what is the average individual sequence length and total number of sequences?  
  > **username_0**: Read length is about 100bp. Wait i need to check the rest. Why is this relevant?  
  > **username_1**: There are easy ways to do a translation on a small number of sequences; it helps to get an idea of scale to gauge what the best approach is. Running an accurate translation on a few sequences is quite different from running a rough translation on millions of sequences.  
  > **username_2**: And what species is this for? Does it have introns and splicing? If so, have you targeted the exons in your sequencing or do those need to be annotated and not translated?  
  
  ---
  
  ## 0 answers
  
  