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BME 110 - Class Calendar

last updated 2/8/2008
Date
Lecture
Topics
 Class Demos/Exercises
Reading
 Problem Sets / Comments
Jan 8, Tu

 Introduction

 Administrative issues, background, goals, overview of course


Ch 1


Jan 10, Th

 Information in genome databases, trends in whole-genome sequencing. A first overview. Explore NCBI resources (Solution given.) Ch 2, 3
Jan 15, Tu Searching for similar sequences
(Slides by T. Lowe)
  • Time to work on in-class exercise from Tu last week.
  • Intro to sequence analysis (BLAST).
  • Assign HW1.
Quick tour/example of the new BLAST form at NCBI
Ch 7 and/or
BLAST tutorial
Jan 17, Th
  • Questions encountered often during work on in-class exercise and problem set 1. A bit of background on COGs, orthologs versus paralogs. What are the key things you should know by now?
  • Time to work on problem set 1 (=HW1) independently
  • General pointers for WWW-bioinformaticians.

    		Ch 14
    Jan 22, Tu Pairwise Alignment Scoring, PSI-BLAST Part I II III (Slides by T. Lowe)
    		Pair-wise alignments and dot plots; BLAST nitty-gritty (Scoring Matrices); PSI-BLAST
    In Class Exercises
    		Ch 8
    Jan 24, Th (Single) Protein Sequence Analysis
    (Slides by C. Rohl)    		 We will soon move on to discuss multiple alignments - however some things can be done with bioinformatics on a single protein sequence. A bit more background info to help with in-class exercise (Jan 22 above) Ch 4, 6 Problem set #1 due
    via WebCT by 4pm (NEW DEADLINE!)
    Jan 29, Tu UCSC Archaeal Genome Browser Guest lecturer David Bernick

  • Problem set #2 (due Friday, Feb 8, 4pm)
    		•
    Jan 31, Th 3-D visualization of protein, RNA Guest lecturer Professor Bill Scott


    Feb 5, Tu
    • How to study for your midterms
    • DNA sequence analysis: (1) a bit on gene finding (also often referred to as gene prediction); most protein sequences in our databases are deduced this way, i.e. they are "putative" proteins, or "hypothetical" proteins. (2) a few practical tools for lab work (restriction analysis, PCR primer design, etc).
    		Ch 5
    Feb 7, Th
    • Issues we noticed during the PSI-BLAST exercise
    • Multiple alignments are key to protein sequence analysis (this will be picked up again later)
    • More protein sequence analysis - motifs, profiles, domains
    		Demo: third part of (revised) in-class exercise from Jan 22 (PSI-BLAST) Ch 9,10
    		 Problem set #2 due via WebCT on Fri Feb 8 by 4pm
    Feb 12, Tu Review Midterm Review (NO CLASS) Homework 1,2 solutions posted.

    Feb 14, Th Midterm EXAM


    Feb 19, Tu
    • MSA: Using, formats, editing (Jalview)
    • Phylo trees: Motivation, creation and bootstrapping.
    		Multiple sequence alignment  demo! Ch 10,13 Homework 3 posted.
    (Helpful for ClustalX color question: amino acid properties/groups)
    HW3 due: March 6, 12:00noon. We may also work on the practical part of the midterm later in the lab.
    Feb 21, Th
    • Part 1 Intro to ncRNAs and structure.
    • Part 2 mFOLD.
    • Part 3 Once you've found an RNA gene..(!).
      (Slides by T. Lowe)
    		RNA-Genomics - what to do when genes are *not* encoding proteins?
    		Ch 12
    Feb 26, Tu
    		Post-exam review of midterm questions, Part I (Written Part) + beginning of Part II (Practical)


    Feb 28, Th
    • Part 4 RNA secondary structure; tRNA, miRNA searches.
    • Post-exam review of midterm questions, cont. with Part II (Practical)
    • Some comments/help on the second (RNA) part of HW3
    		(Ch 12 helps for HW3!)
    Mar 4, Tu
    • Part 1 Protein Data Bank(PDB); HW4 intro
    • Part 2 Components of Protein Structure: From peptide bonds to tertiary structure, and PDB.
    		Protein Structure: Visualization and a bit of Analysis
    		Ch 11 Assign HW4. (due: March 13, 12noon)
    Mar 6, Th
    • Part 3 Protein Structure Analysis (by DL Bernick and CA Rohl)

    		Demo! For structures you can visit PDB. Ch 11
    Mar 11, Tu MaGnET: Malaria Genome Exploration Tool
    www.malariagenomeexplorer.org    		 MaGnET tutorial

    Mar 13, Th
    		Practice questions
    Course Evaluations