Dear computer warriors, EDIT: Sorry, I am new to perl so I don't speak the language so fluently, but what I want to do is this.

I am using an organism called Klebsiella, Kleb for short.
There are many variants. Some are dangerous, and some are not.
I am looking at protein sequences for a protein we can just call protein A
from the dangerous ones (I have about 20 sequences of protein A for this set), as well as about 10 sequences for protein A in the non-dangerous ones.(I have about 30 sequences of protein A for this set).

From the command line I type: ./kleb.pl ATATATA(An amino acid sequence) THe output tells me something like:" There are 7/20 instances found in non-dangerous Kleb. There are 24/30 instances found in non-dangerous Kleb.
"
I will do some statistics on this as well.

What I am looking to do is automate this process so that PERL can merely give me a list of the most commonly found sequences in one or the other set for sequences greater than 4 characters long. It would also be nice to have the capability to do ATA??AA so that the matches don't have to be identical.

to answer bioHishHam, I will check out those modules, thanks!

To answer The Biology Man,
It doesn't matter if they are aligned, I just want to find these characters among them. I have very few sequences, and this data is somewhat confounded by the lineage versus function question, so I have to be able to look at these most common sequences and see if their presence is actually important or they are just a leftover that evoluation has not bothered to alter. In the abstract, a slider window is pretty much what I imagine vetting my sequences, but how to code for it is the problem. My problem is a real lack of perl experience.

The last comment would be helpful but the sequences are about 300 characters; I am looking to find small strings, 4,5,6,7 bp...

In reply to FASTA riddle. by MaroonBalloon

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