problem with sequence alignment

Question

[Parasu]

Hello everyone!

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 very much appreciate it if someone could suggest a method that would solve my problem

(https://imgur.com/a/t1q8ToO) (columns depicted here)

[Wayne]

You aren't describing how you are doing this well enough or what exactly the results are that are causing you trouble?

Your description of how the alignment tool takes them all as a single string doesn't agree with my experience. However, you aren't telling us what alignment tool you are using You are usually allowed to give two pairs separate and then keep doing that. Your submission process seems "off". However, this quick assessment itself may be "off" and just due to lack of clarity in your post.

Also it doesn't sound like you want an alignment tool? (However, your quick description may be making me misunderstand.) Are you looking for intact strings from column A as a string sequence in the strings in column B? That wouldn't be an alignment. That would be matching a pattern, and, in fact, wanting a perfect match. Inherently most programming languages can do this sort of thing where it checks if string A is in string B and tell you the location, i.e., index of the match. Then you can control the output anyway you want. However, because this is common. There's some tools. PatMatch is one I like to use as it allows ambiguity that is biologically-related and works for both nucleic and proteins. (You seem just interested in proteins so you don't have to worry about a complementary strand being in the picture; however, it's often worth it if you are going to learn a tool, to learn one that covers more options.)

These may help you in your endeavor, too:

• Mensur Dlakic's answer to 'How to find the overlapping peptide from a list.'
• Match peptides to protein sequences and tell the position in R
• Perl code to get starting and ending position of list of peptides from the protein sequence of list of protein
• mapping thousands of random k-mer peptides against one protein sequence
• Matching peptides which differ by one letter?
• Running Blastp From Biopython And Only Looking For Exact Matches

General tip:
For asking computational questions, if you are showing an image AND ONLY AN IMAGE in your post, you are probably not helping others help you.