GENOME SEQUENCING AND OBJECTIVES

BYPALLAVI VEDAM

Genomes!!!!!

Bacterial GenomesEukaryotic GenomesHuman Genome ProjectOther Animal and Plant GenomesModel Genomes

Genome Chart

Genome Sequence Databases Availabale

Gene Sequencing???????

Obtaining the Blocks of DNA sequences and assembling serially into contigous stretches of sequence and ulatimately into a Whole Genome sequence using various Bioinformatic strategies is called Genome sequencing.

"The sequence information provides a starting point from which the real research into the thousands of diseases that have a genetic basis can begin," said Venter. "The sooner we can get to this starting point, the sooner we can begin to see a payoff in ultimately improving human health.” This was quoted by Venter who is one of the researchers with the Perkin Elmer working on the Genome sequencing.

Automated DNA sequencing

Sanger Sequencing method:The basic chain termination method, developed by Frederick Sanger in 1974. Generates all possible single-stranded DNA molecules complementary to a given template, and beginning at a common 5' base.

Automated sequencing Method

Still uses Sanger’s chain termination method, but more accurate, and much quicker. Several major advances in the 1980s and 1990s made the automation of Sanger sequencing possible.These new technologies have greatly increased the speed of sequencing, making genome scale sequencing a reality

Reading Sequence Traces

Automated trace reading programs use algorithms to convert trace files into base sequences and assign quality values to each base call in the sequence. They then deposit the information in a databank, all within seconds. One example of such software, available freely, is the phred base-caller developed at the University of Washington

http://www.phrap.org

Contig Assembly

Contig assembly is the finishing step in sequencing a multi-clone stretch of DNA, and involves alignment, editing, and error correction. These tasks are generally done using sequence editing software such as the phrap assembler and the consed graphical editor, also from the University of Washington.

Emerging Sequence Methods

Sequencing by Hybridization (SBH).

Mass Spectrophotometric Sequences.

Direct Visualization of Single DNA Molecules by Atomic force Microscopy (AFM )

Single Molecule Sequencing Techniques

Single nucleotide Cutting Nanopore sequencing Readout of Cellular Gene

Expression

Genome Sequencing

Hierarchical Sequencing.

Shotgun Sequencing

Sequence verification

CompletenessAccuracyValidity of Assembly

Future of Genomics

Individual Genome sequencing via Nanotechnology.

Gina Miller writes "A small British company Solexa is developing a dense single molecule array, based on nanotechnology, that allows simultaneous analysis of hundreds of millions of individual molecules. It expects to apply this technology to sequencing an individual human genome much more quickly and cheaply than can be done with current methods: The arrays could also be applied to studying interactions between other large sets.

Genomic Sequence Advatages and Disadvantages

Normalized coverage of all genes

Information about Gene structure

Information about regulatory Elements

Genome Organization

CostTimeDifficult to

determine if a sequence codes for a Gene.

Future..............

The past 10 years of genetic research has uncovered genes involved in such disorders as cancer, Alzheimer's disease and heart disease. As a result of these discoveries, people now have access to genetic tests that can reveal their risk of serious disease.

Who is doing the sequencing work????

Five centers are doing the bulk of the sequencing work. Three are sponsored by the NIH: The Whitehead Institute/MIT Center for Genome Research in Cambridge, Mass.; Baylor College of Medicine in Houston, Texas; and the Washington University Genome Sequencing Center in St. Louis. The DOE's Joint Genome Institute combines efforts at the Los Alamos, Lawrence Livermore and Lawrence Berkeley national laboratories. A fifth major center is the Sanger Center in Cambridge, England. Another 11 centers around the world also contribute to the sequencing effort.

The NIH and DOE expect to spend $2.8 billion by the time the project is complete in 2003. The cost of sequencing alone will total about $250 million

Conclusion.........

Many improvemnts to the current methods can be definitely done and we as the future Bioinformtists can defintely take this up as a major resposibility.

Thank you........