BBS2214 Introduction to Bioinformatics

1. GENOME SEQUENCING PROJECT by Luvanee Parkianathan, Mahathir Mohmed, Nurul Asyikin Sharuddin, Muhammad Syamil Zahari, and Azman Muin

2. BACKGROUND Genome sequencing projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism requires the DNA sequences for each of the chromosomes in an organism to be determined The information gathered from sequencing will provide the raw data for the exploding field of bioinformatics, where computer science and biology live in symbiotic harmony .

3. FREDERIC SANGER Frederic Sanger is the person that invents “shotgun” sequencing method. This technique involves the separation of fluorescent labelled DNA fragments according to their length on a polyacrilimide gel (PAGE) He is the fourth (and only living) person to have been awarded two Nobel Prizes.

4. SANGER “Shotgun” method

5. The first bacterial genome to be completed was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995 BACKGROUND Human Genome Project starts at 1990 C. elegans finished in 1998, Drosophila melanogaster finished in 2006, the mouse which has less than 1% finished (December 2007: only 20%), and the human which is only 1.5% completed (current: 92%).

6. genome assembly … process of taking a large number of short DNA sequences, all of which were generated by a shotgun sequencing project, and putting them back together to create a representation of the original chromosomes from which the DNA originated "read" by automated sequencing machines, which can read up to 900 nucleotides or bases at a time

7. genome assembly 1 2 3

8. assembly software Phrap AMOS The Celera Assembler The Arachne TIGR Assembler

9. genome annotation … process of attaching biological information to sequences 1 st : identifying elements on the genome, a process called gene finding 2 nd : attaching biological information to these elements. basic level of annotation is using BLAST for finding similarities

10. genome annotation databases Encyclopedia of DNA Elements (ENCODE) Ensembl RefSeq Uniprot

11. plant genome sequencing project Rice

12. plant genome sequencing project

13. animal genome sequencing project Mouse

14. marine genome sequencing project Nanoflagellates

15. Human genome sequencing project

17. The end