Instructor: Vineet Bafna
TAs:
Ryan Kelly
Lectures: TR 2:00-3:20pm. SOLIS 111
Office hours:
Vineet Bafna: By Appointment
TAs Office hours: By appointment.
Course Information:
Announcements
A class mailing list exists at fa05_182@cs.ucsd.edu .
To subscribe, send blank email to fa05_182-subscribe@cs.ucsd.edu. Please send the email from a recognizable UCSD address, or add some details in the message.
Final Exam
Questions (pdf)
Submit electronically by sending mail to the instructor by midnight 12/3/2005.
MIDTERM:
Midterm 1 will be held in class November 1.
Sample Questions
ASSIGNMENTS
| Assignment | Due date | Data |
|---|---|---|
| A1 Note: For problem 1, run with the following parameters: match:1, mismatch:-3, indel: -2 | 10/6 | for Problem 1: human.seq and mouse.seq for Problem 5: two sequences |
| A2 For problem 3, subset F' should be as large as possible. | 10/20 | Family F Family F2 Database D Scoring Matrix |
| A3 Hint: Both S1 and S2 contain post-translational modifications. Common modifications include Methylation of M, Phosphorylation (STY), and Cysteine modifications. | 11/8 | S1 S2 (difficult case) S3 (for de novo, updated 11/5) Protein Prospector |
PROJECTS
| Project | Due date | Data |
|---|---|---|
| Project Descriptions (Updated 11/23) | ||
| C1 | 11/3 | |
| C2 | 11/10 | |
| C3 | 11/24 | |
| C4 | 11/29, 12/1 | File of Spectra InsPecT download |
Lectures
There is no required text for the course. We will use Jones and Pevzner, "An Introduction To Bioinformatics Algorithms", MIT Press, as an optional book.
Future recommended reading is subject to change with little
notice. Please note that the available manuscripts are copyright
protected, and may be used only for educational purposes. The notes
presented here are unedited, and may contain errors. Powerpoint slides
are used only to illustrate examples in class, and are not intended to
substitute lecture notes.
For Biology, the classic reference Molecular Biology of the Cell is now online, although a bit cumbersome to search. We will link to some of the chapters.
| Lecture | Topic | Slides | Suggested Reading |
|---|---|---|---|
| 9/22 | Course outline | L1(pdf) L1(ppt) | Perl 5 guide Bioinformatics Algorithms web-site Chap 3 has a brief introduction to Molecular Biology |
| 9/27 | Sequence Alignment | L2(pdf) L2(ppt) | Notes on DP |
| 9/29 | Keyword match statistics | L3(pdf) L3(ppt) | Notes on L3 Notes on Blast Statistics |
| 10/4 | Scoring Matrices Dictionary Matching Profiles | L4(ppt) | Scoring matrices Dictionary Matching Notes |
| 10/6 | Profiles Regular expression matching Domains | L5(ppt) (Updated 10/11) | ExPASy tools PROSITE |
| 10/11 | Protein Structure Basics Protein sequencing | L6(ppt)(Updated 10/13) | |
| 10/13 | Mass spectrometry analysis Isotope profiles | L7(ppt) | Overview |
| 10/18 | Mass spectrometry analysis De novo sequencing | L8(ppt) | de novo sequencing algorithm |
| 10/20 | Mass spectrometry analysis Quantitation | L9(ppt) | SILAC Map comparison |
| 10/25 | Mass Spec. applications Gene finding basics | L10(ppt) | Cross Linking Transcription (MBC online) Translation (MBC online) |
| 10/27 | Gene finding algorithms | L11(ppt) | GENSCAN Twinscan |
| 11/1 | Midterm 1 | ||
| 11/3 | Gene finding Genome sequencing | L12(ppt) | DNA sequencing Lander Waterman Stats |
| 11/8 | Genome sequencing | L13(ppt) | Arachne (A WGS assembler) |
| 11/10 | Gene Expression | L14(ppt) | Microarray Basics (MBC) |
| 11/15 | Microarray data analysis (classification) | L15(ppt) | |
| 11/17 | Microarray data analysis (dimensionality reduction clustering) | L16(ppt) | |
| 11/22 | Microarray data analysis (clustering) Population Genetics Basics | L17(ppt) | |
| 11/29 | Population Genetics Basics | L18(ppt) | |
Research:
We are always looking for motivated students. If you are interested in
exploring undergraduate research opportunities in Computational
Biology, please email me.