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GENOME SEQUENCING AND

OBJECTIVES

BY

PALLAVI VEDAM

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Genomes!!!!!

Bacterial Genomes

Eukaryotic Genomes

Human Genome Project

Other Animal and Plant Genomes

Model Genomes

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Genome Chart

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Genome Sequence Databases Availabale

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Gene Sequencing???????

Obtaining the Blocks of DNA sequences and assemblingserially into contigous stretches of sequence andulatimately 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 thathave a genetic basis can begin," said Venter. "The sooner

we can get to this starting point, the sooner we can beginto see a payoff in ultimately improving human health.”This was quoted by Venter who is one of the researcherswith the Perkin Elmer working on the Genome

sequencing.

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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.

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Automated sequencing Method

Still uses Sanger’s chaintermination method, butmore accurate, and much

quicker. Several majoradvances in the 1980s and1990s made the automationof Sanger sequencing

possible.These newtechnologies have greatlyincreased the speed of sequencing, makinggenome scale sequencing areality

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Reading Sequence Traces

Automated trace reading programs use algorithms toconvert trace files into base sequences and assignquality values to each base call in the sequence. They

then deposit the information in a databank, all withinseconds. One example of such software, availablefreely, is the phred base-caller developed at theUniversity of Washington

http://www.phrap.org

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Contig Assembly

Contig assembly is the finishing step in sequencing amulti-clone stretch of DNA, and involves alignment,editing, and error correction. These tasks are generally

done using sequence editing software such as the phrapassembler and the consed graphical editor, also from theUniversity of Washington.

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Emerging Sequence Methods

Sequencing byHybridization (SBH).

Mass SpectrophotometricSequences.

Direct Visualization of Single DNA Molecules byAtomic force Microscopy(AFM )

Single MoleculeSequencing Techniques

Single nucleotide Cutting

Nanopore sequencing

Readout of Cellular Gene

Expression

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Genome Sequencing

HierarchicalSequencing.

Shotgun Sequencing

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Sequence verification

Completeness

Accuracy

Validity of Assembly

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Future of Genomics

Individual Genomesequencing viaNanotechnology.

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. Itexpects 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.

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Genomic Sequence Advatages

and Disadvantages

Normalizedcoverage of all

genesInformation about

Gene structure

Information aboutregulatory Elements

Genome

Organization

Cost

Time

Difficult todetermine if asequence codes for

a Gene.

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

The past 10 years of genetic research has uncovered genesinvolved in such disorders as cancer, Alzheimer's disease andheart disease. As a result of these discoveries, people now haveaccess to genetic tests that can reveal their risk of seriousdisease.

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Who is doing the sequencing work????

Five centers are doing the bulk of the sequencing work. Threeare sponsored by the NIH: The Whitehead Institute/MIT Centerfor Genome Research in Cambridge, Mass.; Baylor College of 

Medicine in Houston, Texas; and the Washington UniversityGenome Sequencing Center in St. Louis. The DOE's JointGenome Institute combines efforts at the Los Alamos,Lawrence Livermore and Lawrence Berkeley nationallaboratories. A fifth major center is the Sanger Center in

Cambridge, England. Another 11 centers around the world alsocontribute to the sequencing effort.

The NIH and DOE expect to spend $2.8 billion by the time theproject is complete in 2003. The cost of sequencing alone will

total about $250 million

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Conclusion.........

Many improvemnts to the current methods canbe definitely done and we as the future

Bioinformtists can defintely take this up as amajor resposibility.

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Thank you........