The syllabus is here.
New text is An introduction to Bioinformatics Algorithms by Neil Jones and Pavel Pevezner, MIT Press 2004, ISBN: 0-202-10106-8
Background
SeqAlignment
Fragment Assembly
Phylogenetic Tree
Structure Prediction
A tutorial on HMM
Spring 2006
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Assignment 1 (due 1/19/06)
Assignment 2 (points 30):
(1) Answer the questions on Genebank and Swissprot databses (print
the questions too)
(2) Questions 4.15, 4.16 and 4.17 from the text (p122-3).
(3) Analyze the complexities of the algorithms "BruteForceMotifSearch"
(p 109) and "SimpleMedianSearch" (p113). Do not use book's analyses
even if you arrive at the same results. (due 2/10/06)
Assignment 3 (points 50,
FINALLY Due: May 4, 06)
There will be a guest lecture by Dr. Leonard on Tuesday, February 28.
Projects
--(Due: Presentation on May 2, '06, 7:30-10:30 pm) SEE ANNOUNCEMENT --
Presentation schedule (Room Olin EC 239-240:
System biology: 7:30-8:30 pm. (Gary Hrezo and Weijung Huang)
Protein Docking: 8:30-9:30 pm. (Johannes Nangolo and Christpher Roach)
Correlogram method in protein classification: 9:30-10:30 pm. (Kyle Cacciatore and Stephen Jonsson)
Spring 2005
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Assignment 1 (due 2/8/05): Text Exc. 1, 2, 3 on page 30
Biology Presentation schedule:
Robert Asfar - 2/8/05
Florent launay - 2/8/05
Park Sung Hoon - 2/10/05
Ram, Anjali - 2/10/05
Programming assignment:
Implement Global alignment Dynamic programming algorithm,
(Due: 2/12/05)
Projects.
Project proposal due 3/17/05, Thursday.
Presentations: (BLAST: Rob, PAM: Anjali,
Suffix tree: Park: 3/15/05 Tuesday (15 min)
Quiz on Fragment assembly: 3/24/05 Thursday
I will let you complete it in the next class Thursday 3/31/05, for
about 20 minutes at the end of the class
(Due: 4/20/05 Thursday)
Implement the dynamic programming algorithm for RNA base pairing-prediction
with the simplest assumption. Use alpha values as follows:
alpha(ri,rj)=-2, if (ri,rj)=(A,U) or (U,A) or (G,C) or (C,G),
=0, otherwise. Program should work on any string of length up to 100.
Presentation schedule:
Protein structure prediction: Rob Asfar: 4/14-19/05
Anjali Ram: 4/19-21/05
System biology: Park: 4/21-26/05
PROJECT PRESENTATION: THURSDAY 5/5/05 EXAM TIME
POWER-POINT PRESENTATION+DEMO, MAX 40 MIN, MIN 20 MIN
IN CLASSROOM OR IN MY OFFICE
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Resources:
A decent introduction
to molecular biology by Hunter.
Some information on Human Genome Project is
here.
Some collection of important web databases / tools
prowl.
Conferences:
Intelligent Systems for Molecular Biology
ISMB.
International Conference on Research on Molecular Biology
RECOMB.
IEEE Computational Systems Bioinformatics Conference
CSB.
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A
tutorial on BLAST.
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Spring 2005:
Class Time: Tuesday Thursday 6:30-7:45 pm
Room: E250
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Spring 2003:
(The notes below are primarily from the submissions from the students
in Spring 2003, particularly those from Michael Smith.)
Class schedule: Monday-Wednesday 11 - 12:15 am
Meets at: Room 132EC
Chapter 1: Introduction to Biology
lecture notes.
Some database search procedures: here.
String comparison algorithms: from Cormen et al's Algorithms text book, embedded in my lecture notes on the Algorithms class notes.
Chapter 3: Sequence comparison lecture slides.
Chapter 4: Fragment Assembly lecture slides.
Chapter 6: Phylogenetic Trees lecture notes.
Chapter 8: Molecular Structure Prediction was not covered this time.
Chapter 9: DNA computing lecture slides.
Project description.
A self study done on Sickle Cell Anemia, some notes.
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Spring 2004:
Projects:
Expectation: (1) Literature survey on the current status of the
field evidenced in bibiography development and a presentation(s),
(2) and a software implementation. Both (1) and (2) for the Graduate
Students, and only (2) for the Undergraduate student.
A report of approximately 5 page typed, data from the experiments,
and (outside the 5 pages) source code will be due.
E-mail/CD/ floppy any format is acceptable.
Due date for report submission: April 15 or next class to that date.
System Biology of E-coli cell division process. (Data: Prof. Leonard)
Michel Lacle
Implementation of Blast allignment algorithm and Sequence distance
measurement between Protein chains (subsequently to be expanded
toward usage of Correlogram method of Huang et al, as an MS Thesis).
(Data: Protein Data Bank)
Gandhali Samant
Microarray data clustering algorithm implementation. (Data: ??)
Sunjit Bir
Instance-based learning implementation for clustering sequences.
(Data: Prof. Leonard / PDB)
Manav Rattan
Fragment assembly implementation.(Data: ??) Aditi Gupta
Phylogeny reconstruction implementation. (Data: ??)
Lalit Samant
Helix, sheet (secondary structure) prediction, and solvent accessibility
prediction (1D structure) using DSP and homology modeling techniques.
(Data: PDB)
Seema Gandhi
Deploying matrix method, and dynamic programming method to detect motifs
in some nucleotide sequences and then representing the sequences based on
existing motifs (Ref: Gaurv Tandon's work on computer security).
(Data: Prof. Leonard)
Carl Harroch
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Materials are copyrighted to me (year 2003),
or shared with the acknowledged students, as the case may be.
E-mail:
dmitra@zach.fit.edu