Answers.Body: <p>I don't think that you want an <em>alignment</em> so much as you want to <em>test for the presence of an exact substring</em> (column A) <em>within larger strings</em> (column B).</p>
  <p>There are simple excel utilities that do this, for example the <code>SEARCH()</code> <a href="https://exceljet.net/formula/cell-contains-specific-text" rel="nofollow noreferrer">function</a>. There is no need to use alignments.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-07-13T17:14:56.063Z
Answers.LastActivityDate: 2022-07-13T17:14:56.063Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I'm trying to find if the peptides in column A are present within the longer peptides of column B.</p>
  <p>Pairwise alignment tools take the data from both columns as one string (i.e., TIIDYTNNHYTNNHLEII... and PFYMNITGYTDAYNTDIIDYIIDYTNNHLEIITLFN...) which leads to a number of peptides from column A left unaligned even though the peptide is present within one of the longer peptides in column B.</p>
  <p>I would like to find a method that works for detecting such peptides.</p>
  <p><a href="https://i.sstatic.net/i621I.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/i621I.jpg" alt="columns depicted here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-13T16:11:00.710Z
Comments.Text: Easy, few details are you stuck with a CSV format or prepared to copy and paste column A to one file and column B to another. Its solvable either way.
Comments.UserDisplayName: M__
Tags: <proteins><phylogenetics><sequence>
Title: Problem with sequence alignment
ThreadText: # Problem with sequence alignment
  
  (Asked by: username_0 on 2022-07-13)
  
  I'm trying to find if the peptides in column A are present within the longer peptides of column B.
  
  Pairwise alignment tools take the data from both columns as one string (i.e., TIIDYTNNHYTNNHLEII... and PFYMNITGYTDAYNTDIIDYIIDYTNNHLEIITLFN...) which leads to a number of peptides from column A left unaligned even though the peptide is present within one of the longer peptides in column B.
  
  I would like to find a method that works for detecting such peptides.
  
  [![columns depicted here](https://i.sstatic.net/i621I.jpg)](https://i.sstatic.net/i621I.jpg)
  
  **Tags:** proteins, phylogenetics, sequence
  
  > **Comments:**
  > **username_1**: Easy, few details are you stuck with a CSV format or prepared to copy and paste column A to one file and column B to another. Its solvable either way.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2022-07-13. Score: 3
  
  I don't think that you want an *alignment* so much as you want to *test for the presence of an exact substring* (column A) *within larger strings* (column B).
  
  There are simple excel utilities that do this, for example the `SEARCH()` [function](https://exceljet.net/formula/cell-contains-specific-text). There is no need to use alignments.
  
  
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