This outline is also available in PDF.
Held: Thursday, 10 September 2009
We begin to build our library of procedures that help us ask
interesting (and not so interesting) bioinformatics questions.
- Believe it or not, but we're a little ahead of schedule. We'll see what happens today.
- For Tuesday, you should start reading Chapter 3. Note that there are some spots that are rough going.
- For a week from Tuesday, you should work on the On-your-own project from Section 2.6. (Of course,
in a group of two-to-four.
- Don't forget to sign up for the Bio picnic!
- EC/Support: Watch Ben run at the Les Duke invitational on Saturday.
- CS Table tomorrow (noon, PDR A): A Blind Person's Interactions wtih Technology.
- Compared to the first Web exploration we gave you, these instructions
were much more detailed, and much less open ended.
- Here are some notes, thoughts, and questions
- Did this exploration help you find better ways to look for DNA?
- Does the FASTA file for HBB use the template sequence or the coding
sequence? How do you know?
- Can you find typos in the GenBank record?
- Stupid tidbit: Sam is likely to have an HBB mutation
- What software can you use to compare sequences?
- What procedures would we have to write to make all of this easier to
- There had been questions about the
map is a procedure of two parameters, a procedure
and a list.
- It builds a new list by applying the procedure to each element
of the list.
- We'll do some examples
- Although I haven't mentioned it explicitly, in many cases, you can
treat strings as if they were already lists.
- You can use
map with strings.
- You can use
for val in sequence: with strings
- You can index the elements of strings
- We'll be working a lot with individual elements of lists and strings.
- You get a particular element with
- You get a range of elements with
- You get the first n elements with
- You get all but the first n elements with
- We're going to try a Python variant of guided project 2.5 to get you
ready for on-your-own project 2.6
- What is our overall goal? Simplified sequence alignment
- What do we mean by that?
- Find the best alignment of a short sequence to a long sequence,
allowing one deletion.
- That is, break the short sequence into no more than two parts, and
align them in order. Find the best combination of alignments.
- What are our related goals?
- Think about algorithm design
- Build a library of useful procedures related to sequence alignment
and the central dogma
- Learn more Python!
- Since you're building a library, you should open a single file in which
you're going to put all of your Python code.