<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>

CC BY-SA 4.0
2022-07-13T17:14:56.063Z
2022-07-13T17:14:56.063Z
Maximilian Press
<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>

CC BY-SA 4.0
2022-07-13T16:11:00.710Z
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.
M__
<proteins><phylogenetics><sequence>
Problem with sequence alignment
# 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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