BME 110 Computational Biology Tools: Class Calendar

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BME 110 - Class Calendar

last updated 12/3/2009

Date	Lecture	Topics	Class Demos/Exercises	Reading (B4D)	Problem Sets / Comments
Sep 24, Th				Ch 1 (self-study)	For self-study: What is bioinformatics? General overview and context - note down your questions if you have any!
Sep 29, Tu	Introduction: Overview of topics + HW dates Genome projects and databases (Slides by T. Lowe)	Administrative issues, background, goals, overview of course Information abour genome databases, trends in whole-genome sequencing. A first overview		Ch 2,3
Oct 1, Th	Homework Information	Lecture from Tuesday continued: a bit about genes, and finding them Assign HW1 and work on it during the Evening Section: Part I, 1-5 + Part II, 1-3	Explore NCBI resources		Problem Set #1 Example README file
Oct 6, Tu	Searching for homologous sequences by similarity (Slides by T.Lowe) Problems encountered in hands-on work	Intro to sequence analysis (BLAST) 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		Ch 7 and/or BLAST tutorial AND Usage of different BLAST programs (Guidance notes)
Oct 8, Th	A little more BLAST (Slides by T.Lowe)	(Light) BLAST nitty-gritty	Quick tour/example of the new BLAST form at NCBI
Oct 13, Tu	Introduction and Notes about in-class exercise Taking pair-wise alignment farther: Dotplots, PSI-BLAST (Slides by T.Lowe)	Pair-wise alignments and dot plots; PSI-BLAST Assign HW2 (Part I should be doable now)	In-Class Exercises	Ch 8	HW1 (=Problem Set 1) due via WebCT by 4pm Problem Set #1 answers Problem Set #2
Oct 15, Th	(Single) Protein Sequence Analysis (Slides by C.Rohl) ORFinder notes (see above for Dotlet notes)	Things one can do with a (single) protein sequence (more protein sequence analysis at a later stage)		Ch 6 + Ch 5 is helpful for HW2
Oct 20, Tu	UCSC Archaeal Genome Browser	Guest Lecturer: David Bernick
Oct 22, Th	Multiple Sequence Alignments I (Slides by C.Rohl)	Multiple alignments are key to protein (or any) sequence analysis (Part II to follow)	For Self-Study: Searching Sequence Databases (B4D slides)	Ch 9
Oct 27, Tu	More Protein Sequence Analysis: Multiple Sequence Alignments II	Multiple Alignments Part II: Protein Sequence Analysis in a bit more detail and with examples - motifs, profiles, domains	Demo/in-class: (One way of) Gathering and aligning a protein family, step-by-step		HW2 (=Problem Set 2) due via WebCT by 7pm (slightly extended deadline) Problem Set #2 answers
Oct 29, Th	Lab-related programs (helpful for MT) Midterm preparation tips	Briefly back to DNA - recap gene finding and HW2 programs Midterm: pointeres for how to prepare	For Self-Study: Editing and Publishing Alignments	Ch 10	Evening Section: Q&A in preparation for midterm exam Link 1: mystery-seq-A Link 2: mammoth mitochondrial sequence fragment
Nov 3, Tu		Midterm Review (NO CLASS)
Nov 5, Th	Midterm	EXAM
Nov 10, Tu	Phylogenetic Trees Selecting sequences (why use rRNA?)	Phylogenetic Trees: Motivation, creation of, and bootstrapping Assign HW3 (due November 20)	Demo/in-class (cont. from Oct 27): Multiple Sequence Alignment & Tree for a protein family	Ch 13	Problem Set #3
Nov 12, Th	Intro to ncRNA (Slides by T.Lowe)	RNA Genomics - what to do when genes do not encode proteins?		Ch 12
Nov 17, Tu	More on ncRNAs (Slides by T.Lowe)	More ncRNA particularly on prediction (mfold) (Potentially useful for HW3 Parts II and III) Post-exam review of midterm questions (cont. on Thursday)			NEW! Universal Evolutionary Tree ("Species Tree") available here (possibly helpful for HW3 Part I, questions (f) and (g) - click on picture twice to enlarge).
Nov 19, Th	Even more on ncRNAs (B4D summary)	Post-exam review of midterm questions (cont. from Tuesday) ncRNAs in overview (summary by Bioinformatics4D; for self-study)
Nov 24, Tu	Overview rest of course and HW4	Assign HW4 Time to work on HW3			HW3 (=Problem Set 3) due via WebCT by 12am Thursday (= midnight at the END OF WEDNESDAY) HW4 overview slide HW4 guidelines HW4 server list Note extended deadline, below HW3 solution
Nov 26, Th		Happy Thanksgiving (NO CLASS)
Dec 1, Tu	Protein Structure Basics (B4D) More Protein Structure (Slides by D.Bernick/C.Rohl)	Protein Structure: Overview ... and a little Analysis and Visualization	In-or-after-class, have a look at: Jmol tutorial Protopedia Wiki	Ch 11	Midterm Sequences (for practicing): MT seq1 MT seq2 MT seq3
Dec 3, Th	MaGnET and Java tools	MaGnET: Malaria Genome Exploration Tool www.malariagenomeexplorer.org	MaGnET tutorial (link to tutorial from home page) Course Evaluations Practice Questions (to work on during evening section) mystery sequence		HW4 (see above) due via WebCT by FRIDAY Dec 4, MIDNIGHT (extended deadline)