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Bioinformatics Dr Maha Al-Sulaimani http://fac.ksu.edu.sa/msalsulaimani/home College of Science Department of Biochemistry
Course Outline • Introduction to Bioinformatics. • Search Engines + Tutorial. • Literature Search + Tutorial. • OMIM Database +Tutorial. • Nucleotide Databases. • SNP Database + Tutorial.
Course Outline • Protein Structure (Polyphen) + Tutorial. • Electronic PCR Tutorial. • Alignment Tutorial. • Phylogenetic tree Tutorial.
Grade Distribution • Grade Distribution: • Written Examinations (2): 40 Marks. • Homework: 30 Marks. • Final: 30 Marks.
Exam Dates • Exam Dates: • 1st CAT: Thursday 5/12/1434, 10th of October 2013 from 8-9. • 2nd CAT: Thursday 8/2/1435, 12th of December 2013 from 8-9.
References • Genomics, Proteomics, & Bioinformatics by Campbell and Heyer. • Developing Bioinformatics Computer Skills by Gibas and Jambeck. • Bioinformatics and Functional Genomics by Pevsner, Jonathan.
References • Bioinformatics-Genes, proteins, Computers (2004) by MacDonald CHG. • Essential Bioinformatics (2006) by Xiong, Jin. ISBN-10: 0521600820 1st Ed. • Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (2004) by Baxevanis, AD, Ouellette, BF. ISBN-10: 0471478784
Class Rules Classroom Conduct and Behavior: • Students are expected to adhere to the following rules when attending Biochemistry classes: • Plan to arrive to class on time and to stay for the entire class period (or until dismissed) because random arrivals and exits are disrespectful and distracting(Do not enter class if you are more than 15 minutes late).
Class Rules • All cell phones and other electronic devices (e.g., pagers, iPods, iPads) must be turned off (or on silent) and hidden from view during class time. • Students are responsible for what transpired if they miss a class. It is the student’s responsibility to contact a classmate to determine what was missed.
Class Rules • Talking and other disruptive behaviors are not permitted while classes are in session. • Students are expected to be professional and respectful of other students, instructors and staff. That includes verbal and physical behavior as well as language used in email and phone messages. • No bonus Marks will be given.
Academic Integrity • Academic Integrity • In addition to the above conduct guidelines, students are expected to do original work for all course assignments, including exams. Students are responsible for their own conduct and all cases of dishonesty (e.g., plagiarism, cheating) will be reported to the proper university officials.
What is Bioinformatics? • Bioinformatics is the use of IT in biotechnology for data storage and analysis (Biotechnology?). • It is a mean for analyzing, comparing, graphically displaying, modeling, storing, systemizing, searching, and ultimately distributing biological information. • Includes sequences, structures, function, and phylogeny.
Thus the subject of bioinformatics deals with designing and deploying efficient software tools for accomplishing the previously quoted tasks in a fast and precise manner. • Bridging the gap between the real world of biology and the precise logical nature of computers requires an interdisciplinary perspective.
In Bioinformatics, knowledge of many sciences is required: biology, mathematics, computer science, physics and chemistry. • Bioinformatics is not limited to computing data, but can also solve biological problems (like what? • As it was found that performing all these above-mentioned tasks manually is nearly impossible due to the massive volumes of biological data and the preciseness of works, it became mandatory to use computers for these purposes.
Importance of Bioinformatics • Interprete obtained results. • Analyze the large amounts of biological data. • Storage of Data. • Making it easy to access Data.
Applications of Bioinformatics • Molecular, personal and preventative medicine. • Gene therapy. • Drug development. • Microbial genome applications. • Climate change studies.
Topics in Bioinformatics 1. Human Genome Project: • The draft of the human genome has given us a genetics parts list of what is necessary for building a human: approximately 20,000 genes, their regulatory regions, a lexicon of motifs that are the building block components of proteins and genes, and access to the human variability that make us each different from one another.
Topics in Bioinformatics 2. Proteomics (determining protein structure). 3. Sequence Alignment. 4. Genomics. 5. Evolutionary Biology (Phylogenetics). 6. Systems biology.