CSE 546 Bioinformatics, (2009-2010 autumn)

Instructor: Dr. M. Sakalli

            Class, time: CS Building, 349, Tuesday 1.30:4:30 pm

            E-mail: MSakalli.BioInf.2009 at gmail com.

            Office Hours for requests: Meet me CSE bld, room 325, on Fridays, 11.00 am, to 13.00 pm.

            Evaluation: %50-40 Exam + %20 * 1 Mid term + %10 *3-4 of quizzes.

            Attendance: Full attendance is recommended and your involvement is very much expected.

 

 

The focus:
    1. DNA sequence analysis.
    2. DNA expression analysis. 
    3. The Thermodynamics and Entropic analysis of replication and transcription.

 

Books:
    1. Open web sources will be provided.
    2. Chapters of Mathematical Models in Biology by E. S. Allman
    3. Chapters of Biological Physics by Philip Nelson.
    4. Chapters of Physical Biology of Cell by Rob Philips, Jane Kondev, and Julie Theriot.

Local Bookstore may be: caglayan kitapevi.

 

  

 

Syllabus

Wk no

2009-Autumn Semester

Activities (Subjects, assignments, exams.)

Lecture notes

Log book 

Remarks

1

29/Sept/09

 

2

06/Oct/09

Data Bases.

ppt file

 

 

3

13-20/Oct/09

DNA Characteristics

 4

27/Oct/09

5

 03/Nov/09 Sequence alignment and analysis- part1 ppt file

6

 10/Nov/09 Sequence alignment and analysis- part1 ppt file

7

 16/Nov/09 midterm take home exam pdf file

8

 /Dec/09 Why CpG Islands pdf file Not additinal links are provided here..

Download Instructions from Creig L. Zirbel's Matlab for Chem649 site. Study the 2nd one for RNA and HMM.. And from B. Rodger's Head, HMM stuff..and Chap 13 of E. Alpaydin of Bogazici Univ.

9

       Gambler's ruin, Random walk, and Brownian Motion. all in java from J. Carlson of Utah.

10

Takehome Final Exam .

Below are the two links for the sequences you need to work out. (I made papers ready, alth they could be downloaded from their sites).

PRESENT YOUR PROGRAM at the 1st day of Feb 2010.

1- Paper1, Research in Microbiology, Vol 157, Issue 2, Pages 176-183. Linear plasmid prophage N15 (Enterobacteria phage). A short sequence link Bacteriophage immB region, N15 primase (repA) gene, partial cds; 2795 bp. Download file by clicking Genebank(full) to save ityour computer. Nucleotide sequence is at the bottom of the page starting with ORIGIN.

 

2- Paper2, Unique features of the mitochondrial rolling circle-plasmid mp1 from the higher plant Chenopodium album (L.), Oxford Univ Press 582-590, and the sequence you need to downlod. C.album mitochondrial rolling circle-plasmid mp1. 1309 bp. Remember Genebank(full) to save the file in full gb format to your computer.

 

Links from other universities:

Newly Discovered Genes, Brain Chemicals

 ...