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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

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    $\begingroup$ 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. $\endgroup$
    – M__
    Jul 13, 2022 at 16:11

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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. There is no need to use alignments.

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