Transcript GENOME SEQUENCING AND OBJECTIVES

GENOME SEQUENCING AND
OBJECTIVES
BY
PALLAVI VEDAM
Genomes!!!!!
Bacterial Genomes
Eukaryotic Genomes
Human Genome Project
Other Animal and Plant Genomes
Model 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 singlestranded 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
Completeness
Accuracy
Validity 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
Cost
coverage of all
Time
genes
Difficult to
Information about
determine if a
Gene structure
sequence codes for
Information about
a Gene.
regulatory Elements
Genome
Organization
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........