COT 6936/ CAP 6990
Topics in Algorithms: Bioinformatics/
Bioinformatics Tools
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Professor: Giri NARASIMHAN Office: ECS 389; Phone
348-3748; E-mail: giri@cs.fiu.edu Class: TR 9:30-10:45 AM in Room ECS 136 |
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Course Outline: COT
6936; CAP
6990.
q Reading Material: Click Here.
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Final
Exam: 2-hour exam on Tuesday December 10, 9:30 AM in class. It will be an
Open Book exam (You may bring: the 2 course texts & printouts of class
lectures from the course web page). Questions will be based on whatever was
covered in class (including the student presentations!).
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Homework: Homework
1 (Due 10/2); Homework
2 (Due 10/17); Homework
3 (Due 11/14).
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Frequently
Asked Questions about homework assignments: FAQs
q Presentation Schedule for Project.
q Projects Homepage
(Reports, Presentations) : Click
Here.
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Lecture Transparencies:
(Lectures marked with an * are for both COT 6936 and CAP 6990.)
o * Lecture
1 08/29 [Overview of Bioinformatics]; Relevant
Reading.
o * Lecture
2 09/03 [Molecular Biology Overview]; See Bio-Preliminaries.
o * Lecture
3 09/05 [Statistics Overview]; See Stat-Preliminaries.
o * Lecture
4 09/10 [String Matching & Global Sequence Alignment]; Relevant
Reading.
o * Lecture
5 09/12 [Global/Local Alignment]
o Lecture
6 09/17 [BioPerl, Substitution Matrices, BLAST, FASTA]; Relevant
Reading.
o * Lecture
7 09/19 [Substitution Matrices, BLAST, FASTA]; Relevant
Reading.
o * Lecture
8 09/24 [GenBank, SWISS-PROT, Multiple Alignments]; Relevant
Reading.
o * Lecture
9 09/26 [Hidden Markov Models & Pairwise Alignments]; Relevant
Reading.
o * Lecture
10 10/1 [Hidden Markov Models & HMM Profiles]; Relevant Reading.
o *
Lecture 11
10/3 [Gene Prediction & Protein Structure Basics]; Relevant
Reading.
o
Lecture 12
10/8 [Secondary Structures; Motif Detection; Pattern Discovery]; Relevant
Reading.
o *
Lecture 13
10/10 [Tertiary Structures; Structural Classification]; Relevant
Reading.
o Lecture 14
10/15 [Gene Expression; Hierarchical & K-Means Clustering]; Relevant
Reading.
o * Lecture 15
10/17 [Self-Organizing Maps & Neural Networks]; Relevant
Reading.
o Lecture
16; 10/22 [Decision Trees; SVMs]; Relevant
Reading.
o * Lecture
17; 10/24 [SVMs; Genomics, Proteomics, STS, EST]; Relevant
Reading.
o Lecture
18; 10/29 [Molecular Biology Overview, PCR]; Relevant
Reading.
o * Lecture
19; 10/31 [Gels & 2D-Gels; Sequencing]; Download Multimedia
presentation; Relevant
Reading.
o Lecture
20; 11/5 [Phylogenetic Trees, Distance-based tree construction]; Relevant
Reading.
o * Lecture
21; 11/7 [Phylogenetic Tree Construction: MP & ML Methods]; Relevant
Reading.
o Lecture
22;
11/12 [Perl & BioPerl]; Relevant
Reading.
o * Lecture
23; 11/14 [Genetic Mapping, Physical Mapping, Partial Digest Problem]; Relevant
Reading.
o Lecture
24;
11/19 [Protein Structure Prediction]; Relevant Reading.
o * Lecture 25; 11/21 [Zhan/Zhao,
Deng (Part
I)/Sun (Part
II), Yan,
Cazalis]
o * Lecture 26
o * Lecture 27 03/12; [Wei,
LiangLi,
Buendia,
Rodriguez, Dai/Wu]