Course number: 0418-496
Title: Topics in computer science I: Bioinformatics for computer scientists
Prerequisite:
Location: Lab 3, MCC
Classes: Monday-Wednesday 15:30-16:45
Instructor: Prof. Vince Grolmusz (http://grolmusz.pitgroup.org )
E-mail: grolmusz@pitgroup.org

Offices: KH 32, 3rd floor, Parallel lab, Room 4 (preferred), and KH 31, First floor, Annex, Room 4 (by appointment only).
      
Office hour: Tuesday, 10-11, in Parallel lab   

Teaching assistant: Ms. Fatma fatma@sci.kuniv.edu.kw
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Final results:

Just the grades:


Details:







Literature:

Two books are recommended:
- For a cookbook helping you to navigate between the web databases and webservers: Bioinformatics for dummies, written by Claverie and Notredamme
- For a good coverage of algorithms for computer scientists and a succinct introduction to molecular biology:  An Introduction to Bioinformatics Algorithms, by Jones and Pevzner.
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Course requirements:

There will be 3 project assignments and the final exam. The final grade will consists of the following components:
lAttendance: 10%
l
l3 projects, each: 20%, total: 60%
lFinal exam 40%
That is 110%, the extra 10% is the bonus.
Sample final exam with solutions

•
–
lProjects:

Project 1  Due date has been changed to October 23.
Project 2 is due on November 17.
Project 3 is due on December 16.

Some guidance for Project 1.
Some guidance for project 2.

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Program tools (you may want to install these on your laptop or desktop):

http://code.google.com/p/bamseek/ software for viewing large genomes

PyMoL: a very good molecular visualization tool. For Windows, you need first to install Python from here (either the 32 or the 64 bit version, it depends on your Windows version), then the PyMoL program for the 64 bit version or other versions can be found here: http://www.lfd.uci.edu/~gohlke/pythonlibs/.

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Webservers:

Needleman-Wunsch aligner at EBI: http://www.ebi.ac.uk/Tools/psa/emboss_needle/

Some protein sequences to align: 

>gi|5524211|gb|AAD44166.1| cytochrome b 
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY

 
   ;LCBO - Prolactin precursor - Bovine
   ; a sample sequence in FASTA format
   MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
   EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
   VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
   ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*

   >MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
   ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
   FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
   DIDGDGQVNYEEFVQMMTAK*

Smith-Waterman Aligner (good for understanding the algorithm, 
visualizes the matrix): 

http://www.unm.edu/~rwright/
Protein Sequence Analyzer at PitGroup: http://psa.pitgroup.org

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Talks and Slides:

Week 1:  Biological basics: DNA, RNA, proteins, DNA replication, protein synthesis   Slides_0 
 
Week 2:   DNA sequencing techniques: Sanger and 454/Roche sequencing. Shotgun sequencing. Sequence search algorithms: Naive and Knuth-Morris-Pratt.  Slides_1

Week 3:    Suffix trees. Application of suffix trees. Hamming distance, "Edit-" or Levenshtein distance, finding the edit operators between two sequences. How to optimize? Needleman-Wunsch algorithm and Smith-Waterman algorithm,. Slides_2

Week 4: BLAST algorithm. Slides 3.
 
Week 5:   Slides_6 An application of sequencing and sequence comparisons: Metagenomics.

Week 6:   Slides_7 Protein structure primer
 
Week 7:  Slides_8, Slides_9  Protein X-ray crystallography

Week 8:   Slides_10 The Protein Data Bank  Slides_11 Molecular motors

Week 9:   Slides_12: Molecular docking

Week 10:  Slides_13: Phylogenetic trees

Week 11:  Slides 14: Clustering  Slides 15: The OPTICS clustering

Week 12:  Slides 16: Graphs in biology
Week 13:
Week 14:

Updated on December 22, 2013