Download CSCE590/822 Data Mining Principles and Applications

CSCE555 Bioinformatics
Lecture 2
Meeting: MW 4:00PM-5:15PM SWGN2A21
Instructor: Dr. Jianjun Hu
Course page: http://www.scigen.org/csce555
University of South Carolina
Department of Computer Science and Engineering
2008 www.cse.sc.edu.
Roadmap

DNA, Chromosomes, Genomes

Genome Sequencing and whole genomes

DNA Sequence Representation, Models

Sequence Retrieval, Manipulation

Basic Analysis and Questions of Genomes

Summary
5/23/2017
2
Tools to Learn Concepts Quickly

Wikipedia.org
◦ Search “Genome” bringing up many related
information
◦ In google, type “keywards wiki”

Google search tips
◦ Find info from university websites
 Genome, site:edu
◦ Find info as powerpoint files
 Genome, tutorial, filetype:ppt
DNA

Deoxyribonucleic
acid (DNA) is a
nucleic acid that
contains the genetic
instructions used in
the development and
functioning of all
known living
organisms.
DNA is a long polymer of simple units
called nucleotides
Bases
A: adenosine
C: cytidine
G: guanosine
T: thymidine
Backbone:
sugars and phosphate groups
Microbial Genome: Clostridium sp.
OhILAs
CTGCTGTACTAGGATGCTGGTGGAGAGAGCTGCATATAAATCTTTGAGAGATGCACCAAG
AATCACCATCATGGTTTCCGCCATAGGGGCTTCTTTTTTTATTCAAAATCTTGCCATTGT
TTTATTTGGTGGTAGACCGAAAACTGTTCCAACGGTGGAGGTATTGTCCGGGGTGATAAA
GCTGGGGTCCGTATCTCTACAAAGGCTGACCTTAGTGATTCCAGTAGTAACCATACTGCT
ATTATTTCTTTTGATGTTTTTAGTGAACCAAACGAAAACTGGAATGGCAATGCGTGCCGT
ATCCAAGGACTATGAAACCGCGCGGCTTATGGGAATTGACGTCAATAAAATTATTACCAT
AACCTTTGGTATTGGCTCTGCTCTGGCAGCTATTGGTGGCATCATGTGGGGCGCAAAATT
TCCTAAAATAGACCCTTTTGTTGGGACTATGCCGGGTATTAAATGCTTTATTGCTGCAGT
TCTAGGTGGAATCGGAAACATTCCCGGTGCAGTAATCGGGGGGTTCATCTTAGGGATTGG
AGAGATTATGCTCATTGCTTTTCTACCGAGCCTAACTGGCTATCGAGATGCCTTTGCTTT
CATACTACTGATTATCATTCTACTGTTTAAGCCAACAGGAATCATGGGTGAAAAAATTGC
GGAGAAGGTGTAGACGATGAAAAAGAAAAATACCATATTAACTGGATTAGCAGTATTGCT
TTTATTGATTTATTTGATTTATGCAAATAAGAATTATGATTCTTATAAAATTAGAGTTCT
AAATCTATGTGCAATTTATGCTGTATTGGGACTCAGTATGAATTTGATCAATGGATTTAC
AGGTTTATTTTCCCTTGGACATGCAGGTTTTATGGCAGTAGGTGCCTATACTACCGCTCT
TCTGACCATGACACCGCAAAGTAAGGAGGCAACATTCTTCTTAGTGCCCATTGTAGAGCC
TTTGGCTAAAATTCAGCTTCCTTTTTTTGTGGCACTGATCATCGGTGGACTACTTTCAGC
AATGGTGGCATTTTTAATCGGTGCACCGACTTTAAGGCTGAAGGGCGATTATTTAGCCAT
Complementary Base Pairing:
AT
Write a program to export
CG
complementary sequence?
Genome of organisms

genome of an
organism is a
complete DNA
sequence of one set
of chromosomes
Sequencing: Basic Ideas

Current lab techniques can sequence small (say 700 base pairs) DNA
pieces.
◦ Use restriction enzymes to cut DNA pieces
◦ Sort pieces of different sizes using gel electrophoresis and use the sorting to
read them

Mapping and Walking
◦ Sequence one piece, get 700 letters, make a primer that allowed you to read the
next 700, and work sequentially down the clone
◦ Estimate for human genome sequencing using this method: 100 years

Shotgun sequencing (introduced by Sanger et al. 1977) for sequencing
genomes
◦ Obtain random sequence reads from a genome
◦ Assemble them into contigs on the basis of sequence overlaps
 Straightforward for simple genomes (with no or few repeat sequences)
 Merge reads containing overlapping sequence

Shotgun sequencing is more challenging for complex (repeat-rich)
genomes: two approaches
How Sequencing Works
Beckman CEQ 8000
Sequencing small DNA pieces

G
G
A
T
--------------
A

--------------
C
--------------
T
--------------
T
--------------
A
G
--------------

--------------
T


--------------
A
--------------
C
--------------
A

--------------
G
--------------
G
--------------

A
--------------
A
--------------
A
--------------

C
--------------
T
G
C
---------------------------
Use DNA cloning or PCR to make
multiple copies.
Put in 4 testtubes marked G, A, T and
C
In testtube G use restriction enzymes
that cuts at G.
Do the above step for the other
testubes.
Use gel electrophoresis separately for
the content in each testtube.
The data results in the table on the
left.
Reading the table we get G has
lengths 1, 7, 12, 13, 19; A has lengths 2,
6, 8, 11, 14,15,16; T has length 4, 5, 9,
18 and C has length 3, 10, 17.
This gives us the sequence.
Methods for very large scale sequencing

A hierarchical approach
◦ Map on a large scale (physical mapping), sequence
specific clones whose position in the genome is
known

Shot gun sequencing
◦ “Tear up” the genome and sequence random
fragments until it is done

Sequence tagged connectors (STC)
◦ Sequence the ends of many clones and use this info
to pick overlapping clones
“Shotgun” sequencing
Copy
Clone to sequence
Sequence and “assemble”
….GTCTACCTGTACTGATCTAGC...
…. CCTGTACTGATCTAGCATTA...
…. GTACTGATCTAGCATTACG...
Subclone
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
Whole Genomes of Species
Bacterial Genomes
 Eukaryotic Genomes
 Human Genome Project
 Other Animal and Plant Genomes
 Model Genomes

The genomes of more than 180 organisms
have been sequenced since 1995
http://www.genomenewsnetwork.org/resour
ces/sequenced_genomes/genome_guide_
p1.shtml
Sizes of Genomes
You will learn to download all these
genomes into your computer’s
harddrive
Refer to Table 1.1 Page 2 of Intro
to Comp Genomics book.
Roadmap

DNA, Chromosomes, Genomes

Genome Sequencing and whole genomes

DNA Sequence Representation, Models

Sequence Retrieval, Manipulation

Basic Analysis and Questions of Genomes

Summary
5/23/2017
15
DNA Sequence Representation
DNA Sequence: a string of letters with
alphabet {A, C, G, T}
 Protein sequence: a string of amino acids
with alphabet
{ARNDCEQGHILKMFPSTWYV}

◦ 20 standard amino acids

Genetic code:
Genetic Code: Condon
DNA (ATCG)
RNA (AUCG)
 Three bases of DNA
encode an amino
acid

Genetic Code with Degeneracy
Representation of Sequences

Single DNA sequence
◦ ATCCTTAAGGAAA

Multiple sequences with similarity
◦
◦
◦
◦
◦
Regular Expression
ATAAA
ACAAAA
ATAAAAAA
A[TC]A+
Representation of Sequences

Probablistic Model: Position-specific
scoring matrices (PSSM)
Representation of Sequence:
FASTA format
text-based format for representing either
nucleic acid sequences or peptide
sequences,
 allows for sequence names and comments
to precede the sequences.

Roadmap

DNA, Chromosomes, Genomes

Genome Sequencing and whole genomes

DNA Sequence Representation, Models

Sequence Retrieval, Manipulation

Basic Analysis and Questions of Genomes

Summary
5/23/2017
22
Sequence Retrieval, Manipulation

Where to download genome/sequence
data
◦ Online databases: EMBL, GenBank
◦ Entrez cross-database search (life science
search engine)
◦ Goolge -
Example: Download H. influenzae
Genome
First bacterial genome: H. influenzae,
1830Kb
 http://www.ncbi.nlm.nih.gov/sites/entrez


NC_007146
LinksHaemophilus influenzae 86-028NP, complete genome
DNA; circular; Length: 1,914,490 nt
Replicon Type: chromosome
Created: 2005/06/27
Genome Information of H.
influenzae
Download the Complete Genome
Sequence in Fasta Format
Roadmap

DNA, Chromosomes, Genomes

Genome Sequencing and whole genomes

DNA Sequence Representation, Models

Sequence Retrieval, Manipulation

Basic Analysis and Questions of Genomes

Summary
5/23/2017
28
Simple Questions and Analysis of
Genome Sequence
Frequencies of Bases A/C/G/T by simple
counting
 Sliding windows to check local density
 AT AG AC TA TG TC


K-mers frequent/unusual words
◦ 2-mers AT AG AC TA TG TC etc.
◦ 3-mers
Genomic landscape: GC
content analysis
The overall GC content of the human
genome is 41%.
 A plot of GC content versus number of
20 kb windows shows a broad profile
with skewing to the right.

Page 627
GC content of the human genome: mean 41%
Source: IHGSC (2001)
Fig. 17.15
Page 628
Genomic landscape: CpG islands
Dinucleotides of CpG are under-represented in genomic
DNA, occuring at one fifth the expected frequency.
 CpG dinucleotides are often methylated on cytosine (and
subsequently may be deamination to thymine).


Methylated CpG residues are often associated with housekeeping genes in the promoter and exonic regions.
Methyl-CpG binding proteins recruit histone deacetylases
and are thus responsible for transcriptional repression.
 They have roles in gene silencing, genomic imprinting, and Xchromosome inactivation.

Broad genomic landscape: CpG
islands

Findings:
◦ 50,267 CpG islands in human genome
◦ 28,890 after masking repeats with
RepeatMasker
◦ 5-15 CpG islands per megabase
◦ (about <40 genes per megabase)
Summary
DNA, Chromosome, Genome
 Sequence models
 Sequence database, retrieval
 Whole genome sequence analysis

Slides Credits

Slides in this presentation are partially
based on the work of slides from
Internet.