# Class 05: The Central Dogma (2)

Back to The Central Dogma (1). On to Gene Alignments (1).

This outline is also available in PDF.

Held: Thursday, 10 September 2009

Summary: We begin to build our library of procedures that help us ask interesting (and not so interesting) bioinformatics questions.

Related Pages:

Notes:

• 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, on-your-own means in a group of two-to-four.
• 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.

Overview:

## Web Exploration, Discussed

• Compared to the first Web exploration we gave you, these instructions were much more detailed, and much less open ended.
• Was that good, bad, ...?
• 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 do?

## Detour: Some Python

• There had been questions about the `map` procedure.
• `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 `lst[position]`.
• You get a range of elements with `lst[start:after]`
• You get the first n elements with `lst[:n]`
• You get all but the first n elements with `lst[n:]`

## Guided Exercise

• 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?
• Build a library of useful procedures related to sequence alignment and the central dogma
• Since you're building a library, you should open a single file in which you're going to put all of your Python code.

Back to The Central Dogma (1). On to Gene Alignments (1).

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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Samuel A. Rebelsky, rebelsky@grinnell.edu

Copyright © 2009 Vida Praitis and Samuel A. Rebelsky. This work is licensed under a Creative Commons Attribution-NonCommercial 2.5 License. To view a copy of this license, visit `http://creativecommons.org/licenses/by-nc/2.5/` or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.