Hello everyone!
This is my first post on here. Hope you guys can give a helping hand to me.
This semester I'm getting a computational biology course. I've been enjoying though being a biochemistry based student makes dealing with calculations and maths a bit challenging.
There's this homework I'm struggling with: http://web.iyte.edu.tr/~bilgekaracali/EE550/Homework%201.pdf
Even though I'm reading the text book I can't manage to find out how I am going to create PAM and BLOSUM matrices from the aminoacid sequence given.
Can you show me a way out as I will keep searching for such examples but solved?
Thank you and sorry if I'm breaking some kind of forum rules by posting this, I just started to feel overwhelmed.
1 answer
- https://web.archive.org/web/20130726133541/http://biorecipes.com/Dayhoff/code.html
- http://www.perlmonks.org/?node_id=1049813
- http://books.google.com/books?id=C88KrD4enWkC&pg=PA68&hl=en#v=onepage&q&f=false
- http://books.google.com/books?id=bvY21DGa1OwC&pg=PA96&source=gbs_toc_r&cad=2#v=onepage&q&f=false
- How To Create Pam Or Blossum Matrix (Substitution Matrix)
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Hi,
Though we don't encourage solving your homework for you, helping you out with pointers would not be a problem.
A small note: From the way you've phrased your question, it would seem that you think of the sequence in the assignment as a single sequence. Please note that each line is a different sequence and you have 20 sequences, each 100 aa long. This should help you with your first step towards building the matrices.