# Problem with sequence alignment

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.

• 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__
Jul 13, 2022 at 16:11

There are simple excel utilities that do this, for example the SEARCH() function. There is no need to use alignments.