Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. It only takes a minute to sign up.
Sign up to join this community
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.
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.
