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BME 110 - Class Calendar

last updated 3/10/2009
Date
Lecture
Topics
 Class Demos/Exercises
Reading (B4D)
 Problem Sets / Comments
Jan 6, Tu
  • Introduction
  • Twelve commandments of WWW-bioinformatics
    • Administrative issues, background, goals, overview of course
    • General pointers for WWW-bioinformaticians.



    		Ch 1


    Jan 8, Th
  • More housekeeping (HW dates)
  • Genome projects and databases
    (Slides by T.Lowe)
    • Information in genome databases, trends in whole-genome sequencing. A first overview.
    • NCBI overview and resources.
    		 Explore NCBI resources (Guidance notes/sample solution given.) Ch 2, 3
    Jan 13, Tu
  • Searching for homologous sequences by similarity
    (Slides by T.Lowe)
  • Homework information
    • Intro to sequence analysis (BLAST).
    • Assign HW1.
    		Quick tour/example of the new BLAST form at NCBI
    		 Ch 7 and/or BLAST tutorial
    Jan 15, Th
  • Problems encountered in hands-on work
  • A little more BLAST
    (Slides by T.Lowe)
    		•
    • Questions encountered often during work on in-class exercise. A bit of background on COGs, orthologs versus paralogs. Key things you should know by now.
    • (Light) BLAST nitty-gritty.


    Jan 20, Tu
    • Hands-on work on HW1 (with tutors)



    Jan 22, Th
  • Taking pairwise alignment farther: Dotplots, PSI-BLAST (Slides by T.Lowe)
    • Pair-wise alignments and dot plots; PSI-BLAST
    • Assign HW2

    		In Class Exercises
    		Ch 8
    (+ Ch 5 is helpful for HW2)    		 Problem set #1 due via WebCT by 4pm (EXTENDED DEADLINE)
    Jan 27, Tu
  • Brief additional notes on using PSI-BLAST at NCBI
  • (Single) Protein Sequence Analysis
    (Slides by C.Rohl)
    		•
    • Things one can do with a (single) protein sequence (more protein sequence analysis at a later stage)
    		 For Self-Study: Searching Sequence Databases

    Jan 29, Th
  • UCSC Archaeal Genome Browser
    Part I; Part II
    		•


    Feb 3, Tu
  • Introduction and ORFfinder notes
  • Multiple Sequence Alignments I
    (Slides by C.Rohl)
    • Multiple alignments are key to protein (or any) sequence analysis (Part II to follow)
    		Demo: ClustalX (if we have time) Ch 9,10
    		 Problem set #2 due via WebCT by WEDNESDAY Feb 4, midnight (EXTENDED+FINAL deadline)
    Feb 5, Th
  • Midterm Preparation
  • Multiple Sequence Alignments II: (More) Protein Sequence Analysis (worked through first half of slides in class)
    • Midterm: pointers for how to prepare
    • Multiple Alignments Part II: Protein Sequence Analysis in a bit more detail and with examples - motifs, profiles, domains
    		 (1)Demo/in-class: (One way of) Gathering and aligning a protein family, step-by-step
    (2)For Self-Study: Editing and Publishing Alignments
    		 Ch 10 (again)
    		 Evening Section: HW2 and midterm questions review (prep for midterm)
    Feb 10, Tu
    		Midterm Review by yourselves (NO CLASS)

    Feb 12, Th Midterm EXAM


    Feb 17, Tu
  • Introduction Slide
  • Continuation of lecture from Feb 5 (Multiple Sequence Alignments II)
  • Phylogenetic Trees
    		•
    • (cont. from Feb 5) Motifs, profiles, domains
    • Phylogenetic Trees: Motivation, creation of, and bootstrapping (addendum: Why use rRNA)


    		Ch 13
    Feb 19, Th
  • Gene Finding
    • DNA sequence analysis that is often relevant and useful for laboratory work (back-relates to Homework 2)
    • Assign HW3

    		In-class: Multiple Sequence Alignment & Tree for a protein family (follow-on from Feb 5)
    		Ch 5
    Feb 24, Tu
  • Intro to ncRNAs
    (Slides by T.Lowe)
    		•
    • RNA Genomics - what to do when genes do *not* encode proteins?
    • Post-exam review of midterm questions (cont. on Thursday)


    		Ch 12
    Feb 26, Th




    Mar 3, Tu
  • More on ncRNAs
    (B4D)
  • Even more on ncRNAs
    (Slides by T.Lowe)
    		•
    • ncRNAs in overview (by Bioinformatics4D)
    • mfold (Potentially useful for HW3 Parts II and III)

    		Scoring Matrices explained
    Online Slides from Weizmann Institute course
    		NEW! Universal Evolutionary Tree ("Species Tree") available here
    (possibly helpful for HW3 Part I, questions (f) and (g) - click on picture twice to enlarge).
    Mar 5, Th
  • Protein Structure Basics
    (B4D}
  • More Protein Structure
    (Slides by D.Bernick/C.Rohl)
    		•
    • Protein Structure: Overview
    • ... and a little Analysis and Visualization
    • Assign HW4

    		In-class:
    		Ch 11
    		 Problem set #3 due via WebCT by 4pm (BEFORE CLASS)
    Mar 10, Tu Introduction slides
    MaGnET and Java tools
    		MaGnET: Malaria Genome Exploration Tool
    www.malariagenomeexplorer.org    		 MaGnET tutorial


    Mar 12, Th

    		Practice questions
    Course Evaluations    		 HW4 (see above) due via WebCT by FRIDAY Mar 13, 5pm