Bioinformatics Models and Algorithms

Fall 2009 - BGSU - Math 4000 - Math 5820

Until the Blackboard shell is available, I will post some relevant information here.

The announcement of the course is the best general overview of the course.

Workshop handouts on dynamic programming

I have run a few workshops over the last few years which introduce people to the most basic ideas of dynamic programming.  See this page.

Textbook

The textbook will be An introduction to bioinformatics algorithms by Jones and Pevzner.  You can preview it at books.google.com, but you cannot read the whole book there. You should get the book and read Chapters 1-3 as soon as you can; before the semester starts, if possible.  In Chapter 1, sit and think about the game between Alice and Bob, and see if you can figure out the matrix on page 2.  This is explained better in Section 2.9.4.  Chapter 2 will be familiar to people with a Computer Science background; those who haven't taken much CS should try to read it.  Chapter 3 is a brief overview of molecular biology that most of you will benefit from.

Learn to program if you don't already know how

If you do not already know how to write programs that use for loops and while loops, please see the following pages and start practicing:

• Learn to program with Matlab or Octave to learn how to write simple programs
• Read about Matlab and Octave and learn the syntax of their commands with these tutorials I've written.  This page also tells how to download Octave.

Learn some molecular biology

Most of the students registered for the course are not Biology majors, and so will benefit from learning some basic elements of biology that will be relevant to the course.  I've compiled a list of terms that I will expect you to know after the first few weeks of the course.  I suggest that you start doing web searches for these terms and accumulate descriptions of them for yourself.  I've typed them up in an Excel sheet; you might want to type in definitions next to them and paste in pictures as well.

Here is the current list; I will add terms to the bottom of the list as time goes on:

RNA; RNA secondary structure
RNA tertiary structure
DNA
Polymerase chain reaction (PCR)
Amino acid
Protein
Promoter
Gene
DNA transcription
Transcriptome
Messenger RNA
Protein translation
Ribosome
Intron and Exon
Ribozyme
Non-coding RNA
BLAST
Riboswitch
microRNA
Polypeptide
Ligand
Phylogeny
Domains of life