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Introduction to Bioinformatics
Lecturer: Prof. Yael Mandel-Gutfreund
Teaching Assistance:
Rachelly Normand
Edward Vitkin
Course web site :http://webcourse.cs.technion.ac.il/236523
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What is Bioinformatics?
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Course Objectives
• To introduce the bioinfomatics discipline • To make the students familiar with the major
biological questions which can be addressed by bioinformatics tools
• To introduce the major tools used for sequence and structure analysis and explain in general how they work (limitation etc..)
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Course Structure and Requirements
1.Class Structure1. 2 hours Lecture 2. 1 hour tutorial
2. Home work• Homework assignments will be given every second
week• The homework will be done in pairs.• 5/5 homework assignments will be submitted
2. A final project will be conducted in pairs * Project will be presented as a poster –poster day 19.3
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Grading
• 20 % Homework assignments
• 80 % final project
(10% proposal,
20% supervisor evaluation
70% poster presentation)
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Literature list• Mount, D.W. Bioinformatics: Sequence and Genome
Analysis. 2nd ed.,Cold Spring Harbor Laboratory Press, 2004.
Advanced Reading
Jones N.C & Pevzner P.A. An introduction to Bioinformatics algorithms MIT Press, 2004
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What is Bioinformatics?
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“The field of science in which biology, computer science, and information technology merge to form a single discipline”
Ultimate goal: to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned.
What is Bioinformatics?
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Central Paradigm in Molecular Biology
mRNAGene (DNA) Protein
21ST centaury
Genome Transcriptome Proteome
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From DNA to Genome
Watson and Crick DNA model 1955
1960
1965
1970
1975
1980
1985
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1995
1990
2000 First human genome draft
First genomeHemophilus Influenzae
Yeast genome
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Total 1379 294
Eukaryotes 133 39
Bacteria 1152 235
Archaea 94 23
Complete Genomes
2010 2005
Total complete genomes 10.10.13 = 7381
1,000 Genomes Project: Expanding the Map of Human Genetics
Researchers hope the effort will speed up the discovery of many diseases's genetic roots
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Main Goal:
To understand the living cell
Annotation Comparativegenomics
Functionalgenomics
25000 genomes… What’s Next ?
The “post-genomics” The “post-genomics” eraera
SystemsBiology
And beyond…Personalized medicine
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From ….25000 genomes
To…Understanding living cells
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CCTGACAAATTCGACGTGCGGCATTGCATGCAGACGTGCATG
CGTGCAAATAATCAATGTGGACTTTTCTGCGATTATGGAAGAA
CTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTC
AGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGA
AGAGCCAGTAAAAGACGCAGTGACGGAGATGTCTGATG CAA
TAT GGA CAA TTG GTT TCT TCT CTG AAT ......
.............. TGAAAAACGTA
Annotation
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Annotation
Identify the genes within a given sequence of DNA
Identify the sitesWhich regulate the gene
Predict the functionWhat do they do???
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How do we identify a genein a genome?
A gene is characterized by several features (promoter, ORF…)some are easier and some harder to detect…
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Using Bioinformatics approaches for Gene hunting
Relative easy in simple organisms (e.g. bacteria)
VERY HARD for higher organism (e.g. humans)
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Comparativegenomics
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Comparison between the full drafts of the human and chimp genomesrevealed that they differ only by 1.23%
How can we be so similar--and yet so different?
How humans are chimps?
Perhaps not surprising!!!
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Where are we different ??
Where are we similar ???
VERY SIMAILARConserved between many organisms
VERYDIFFERENT
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Human ATAGCGGGGGGATGCGGGCCCTATACCCChimp ATAGGGG--GGATGCGGGCCCTATACCCMouse ATAGCG---GGATGCGGCGC-TATACC-A
Human ATAGCGGGGGGATGCGGGCCCTATACCCChimp ATAGGGGGGATGCGGGCCCTATACCCMouse ATAGCGGGATGCGGCGCTATACCA
Sometime minor changes in critical genes can make a big difference
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Single change in a genes among humans can be responsible for sever diseases
Sickle Cell Anemia
Due to 1 swapping of an A for a T
Image source: http://www.cc.nih.gov/ccc/ccnews/nov99/
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Healthy Individual>gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA
GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC
>gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens]
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH
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Diseased Individual>gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA
GGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC
>gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens]
MVHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG
AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH
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Functionalgenomics
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TO BE IS NOT ENOUGH In any time point a gene can be functional or not
The difference in the brain size between Human and apes is mainly related to the different levels of the genes expression and not their content
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Systems Biology
Jeong et al. Nature 411, 41 - 42 (2001)
Biological networks
What can we learn from Biological Networks
• Is the protein essential for the organism ?• Is it a good drug targets?
What can we learn about this protein
How can bioinformatics contribute to Medicine?
http://www.tedmed.com/talks/show?id=17961
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What of all this will we learn in the course?
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The course will concentrate on the bioinformatics tools and databases which are used to :- Annotate genes, - Compare genes and genomes- Infer the function of the genes and proteins- Analyze the interactions between genes and proteinsETC….
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Main Topics
1. Introduction to bioinformatics2. Pairwise alignment3. Database search4. Protein alignments5. MSA and phylogenetic analysis6. Sequencing7. Motif search-function prediction8. Gene expression9. Structural bioinformatics (proteins and RNA)10. Biological networks