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BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 1
Lecture 1
What is Bioinformatics?
(Genomics? Computational Biology?)
#1_Aug
BCB 444/
Thanks to Mark Gerstein (Yale) & Eric Green (NIH) for many borrowed & modified PPTs BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 2 BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 3
Introduction to Bioinformatics
Instructors: Drena Dobbs [email protected] Michael Terribilini [email protected] Jae-Hyung Lee [email protected] TAs: Jeff Sander [email protected] Pete Zaback [email protected] Lab: MBB 106, 4-
BCB 444/
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 4
BCB 444/544 - Website
http://bindr.gdcb.iastate.edu/bcb
- Syllabus
- Lecture & Lab Schedules
(with Homework Assignments)
- Lecture PPTs
- Lab Exercises
- Practice Exams
- Grading Policy
- Project Guidelines, etc.
- Links
- Check regularly for updates! BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 5
Meets in 1304 MBB every week
EXCEPT this week:
Current schedule: Thurs 1-3 PM
Conflicts?
Alternatives?
BCB 444/544 - Computer Lab
1st Lab meets in Library Rm 32
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 6
Essential Bioinformatics
Jin Xiong, Cambridge, 2006
ISBN-13: 9780521600828
Textbook Companion Website:
Not much of one for Xiong: Xiong resources but check out companion sites for optional texts (next slide - URLs also provided on class website)
BCB 444/544 - Required Textbook
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 7
BCB 444/544 - Optional Textbooks
Please don't buy these yet! Completely optional, perhaps useful, references. All are available from ISU Bookstore but are cheaper from online booksellers.
- Mount - good reference for both "biologists" and "computer scientists" - but a bit out of date; Online resources - include lists of applications with URLs
- Pevsner - great overview, esp. for those with little biology background; Online resources - excellent: many links & PPTs.
- Jones & Pevzner - good introduction to basic algorithms, esp. for biologists with little computer science background; Online resources - very good: problems, links & PPTs. BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 8
Required Reading
(after today, must read before lecture)
Wed Aug 22 - for Lecture
- Xiong Textbook:
- Chp 1 - Introduction
- Chp 2 - Biological Databases
Thurs Aug 23 - for Lab #1:
- Literature Resources for Bioinformatics
Andrea Dinkelman, see Lab Schedule for URL
Fri Aug 24
- Genomics & Its Impact on Science & Society:
Genomics & Human Genome Project Primer
see Lecture Schedule for URL
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 9
Xiong: Chps 1 & 2
SECTION I INTRODUCTION AND BIOLOGICAL DATABASES 1 Introduction What Is Bioinformatics? Goal Scope Applications Limitations New Themes Further Reading 2 Introduction to Biological Databases What Is a Database? Types of Databases Biological Databases Pitfalls of Biological Databases Information Retrieval from Biological Databases Summary Further Reading BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 10
Assignment #1:
Tell us about you
Due: Wed, Aug 22
1- Complete HW1_Aug20 for Drena
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 11
A tutorial on genomic sequencing, gene structure,
genes prediction
Howard Hughes Medical Institute (HHMI)
Cold Spring Harbor Laboratory (CSHL)
Assignment #2 (& for Fun):
DNA Interactive "Genomes"
1. Take the Tour
2. Read about the Project
3. Do some Genome Mining with:
ļ Nothing to turn in - just do it!
http://www.dnai.org/c/index.html
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 12
What is Bioinformatics?
Wikipedia:
- Bioinformatics and computational biology involve the use of techniques including: applied mathematics informatics statistics computer science artificial intelligence chemistry & biochemistry (& engineering) to solve biological problems usually on the molecular level
- Research in computational biology often overlaps with
systems biology (& genomics )
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 19
Molecular Biology Information:
Protein Sequences
- Biocatalysis
- Cofactor transport/storage
- Mechanical motion/support
- Immune protection
- Regulation of growth and differentiation
Information:
- 20 letter alphabet: ACDEFGHIKLMNPQRSTVWY of amino acids (aa)
- ~ 300 aa in an average protein (in bacteria)
3 X 10^6 known protein sequences Protein sequences:
d1dhfa_ d8dfr__ LNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTLNSIVAVCQNMGIGKDGNLPWPPLRNEYKYFQRMTS d4dfra_ d3dfr__ ISLIAALAVDRVIGMENAMPWN-LPADLAWFKRNTLTAFLWAQDRDGLIGKDGHLPWH-LPDDLHYFRAQTV
Functions: Most cellular functions are either performed by or
regulated by proteins
- What is this protein?
- Which amino acids are most important for folding, activity, or interaction with other proteins?
- Which sequence variations are harmful (or beneficial)? Modified from Mark Gerstein BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 20
Molecular Biology Information:
Macromolecular Structures
Modified from Mark Gerstein
DNA/RNA/Protein Structures
- How does a protein (or RNA) sequence fold into an active 3-D structure?
- Can we predict structure from sequence?
- Can we predict function from structure (or perhaps, from sequence alone?) BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 21
We don't understand the protein folding code yet -
but we try to engineer proteins anyway!
Modified from Mark Gerstein BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 22
Molecular Biology Information:
Biological Processes
- How do patterns of gene expression determine phenotype?
- Which genes and proteins are required for differentiation during during development?
- How do proteins interact in biological networks?
- Which genes and pathways have been most highly conserved during evolution?
Genomics & Systems Biology
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 23
"On a Large Scale?"
Whole Genome Sequencing
Genome sequences now accumulate so
quickly that, in less than a week, a single
laboratory can produce more bits of data
than Shakespeare managed in a lifetime,
although the latter make better reading.
-- G A Pekso, Nature 401 : 115-116 (1999) Modified from Mark Gerstein
1st a complete bacterial genome,
then yeast
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 24
Genome Projects:
Rapid Automated Sequencing
Another recent improvement: rapid & high resolution separation of fragments in capillaries instead of gels E Yeung, Ames Lab, ISU Modified from Eric Green More recently? Pyro-sequencing 454 sequencing http://www.454.com/ $ 1000 genomes?
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 25
1st Draft Human Genome:
"Finished" in 2001
Modified from Eric Green BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 26
Human Genome Sequencing
Two approaches:
- Public (government) - International Consortium
(mainly 6 countries, NIH-funded in US)
- Hierarchical cloning & BAC-to-BAC sequencing
- Map-based assembly
- Private (industry) - Celera, Craig Venter, CEO
- Whole genome random "shotgun" sequencing
- Computational assembly (took advantage of public maps & sequences, too)
Guess which human genome they sequenced? Craig's
How many genes? ~^ 20,000 (Science, May 2007)
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Public Sequencing:
International Consortium
Modified from Eric Green BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 28
So, having a list of parts is not enough!
BIG QUESTION?
SYSTEMS BIOLOGY
How do parts work together to form a
functional system?
What is a system? Macromolecular complex, pathway,
network, cell, tissue, organism, ecosystemā¦
BCB 444/544 F07 ISU Dobbs #1 - What is Bioinformatics? 8/20/07 29
Is this Bioinformatics?
- Creating digital libraries
- Automated bibliographic search and text comparison
- Knowledge bases for biological literature
- Methods for structure determination
- Computational X-ray crystallography
- NMR structure determination
- Metabolic pathway simulation
YES
YES
YES
Modified from Mark Gerstein BCB 444/544 F07 ISU^ Dobbs #1 - What is Bioinformatics?^ 8/20/07^30
- Gene identification by sequence inspection
- Prediction of splice sites, promoters, etc.
- DNA methods in forensics
- Modeling populations of organisms
- Genomic sequencing methods
- Assembling contigs
- Physical and genetic mapping
- Linkage analysis
- Linking specific genes to various traits
YES
YES
YES
YES
YES
Modified from Mark Gerstein
Is this Bioinformatics?
