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Transcript 
Bioinformatics & Biology
Andreas Gisel
IITA – Bioscience & Bioinformatics
A member of CGIAR c onsortium
www.iita.org
Andreas Gisel
Bioinformatics specialist at IITA
Institute for Biomedical Technologies, Italy
Novartis SA, pharmaceutical company, Switzerland
Trained as Molecular Biologist Novartis SA, pharmaceutical company, Switzerland
University of California, Berkeley
Federal Institute of Technology, Switzerland A member of CGIAR c onsortium
www.iita.org
Bioinformatics -­ definition
Bio – Biology, Life Sciences
DATA
INTERPRETATIONS
Informatics – computational sciences
A member of CGIAR c onsortium
RESULTS
Bio informatics
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Bioinformatics -­ definition
Bio – Biology, Life Sciences
INTERPRETATIONS
Informatics – computational sciences
RESULTS
DATA
Knowledge
Data Repositories
A member of CGIAR c onsortium
www.iita.org
Basic Biology
Life
The condition that distinguishes organisms
from inorganic objects and dead
organisms, being manifested by
Ø growth through metabolism,
Ø reproduction,
Ø and the power of adaptation to
environment through changes
originating internally.
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Basic Biology
Life
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Basic Biology
Cell
The cell (from Latin cella, meaning "small room") is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, and cells are often called the "building blocks of life".
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Basic Biology
Cell
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Basic Biology
DNA (Deoxyribonucleic acid), carrier of information
RNA (Ribodeoxynucleic acid), transported of information
Protein, functional unit orchestrating the cell functionality and cell division
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Basic Biology -­ DNA
DNA (Deoxyribonucleic acid), carrier of information
Up to hundreds of millions of nucleotides
4 nucleotide
Guanine
Cytosine
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Adenine
Thymidine
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Basic Biology -­ DNA
DNA (Deoxyribonucleic acid), carrier of information
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Basic Biology -­ RNA
RNA (Ribodeoxynucleic acid), transported of information
4 nucleotide
Guanine
Cytosine
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Adenine
Uracil
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Basic Biology -­ RNA
RNA (Ribodeoxynucleic acid), transported of information
RNA folding
Alternative splicing
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Basic Biology -­ Protein
Protein, functional unit orchestrating the cell functionality and cell division
20 amino acids
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Basic Biology -­ Protein
Protein, functional unit orchestrating the cell functionality and cell division
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Basic Biology – Genetic Code
How to translate the 4 letter code of the RNA into a 20 letter protein code?
It would require a minimum of three DNA nucleotides to "spell out" one amino acid, and indeed this is the number that is actually used.
Any single set of three nucleotides is called a codon, and the set of all possible three-­
nucleotide combinations is called "the genetic code" or "triplet code." There are sixty-­four different combinations or codons (4 × 4 × 4 = 64).
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Basic Biology – Genetic Code
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Basic Biology -­ Systems
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Basic Biology -­ Systems
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Basic Biology -­ Sequencing
Sequencing is the process of determining the precise order of nucleotides within a DNA molecule or order of amino acids in a protein molecule.
² First fully sequenced bio-­sequence
² amino acid of insulin (51aa) 1955
² First fully sequence nucleic acid
² tRNA (75nt) 1965
² First DNA
² Bacteriophage (5375nt) 1977
² DNA sequencing
² Sanger sequencing technology (1975)
² Pyrosequencing (Next Generation sequencing 2004)
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Basic Biology -­ Sequencing
Sequencing is the process of determining the precise order of nucleotides within a DNA molecule or order of amino acids in a protein molecule.
DNA
ATGTCTGGGCTTGTGGGCTTGCTTGTGGGTCTTGTGCTGGTGGGTT
CTGTTAGCTCAGCGAAATTCGATGAGCTATTTCAACCCGGCTGGGC
RNA
AUGUCUGGGCUUGUGGGCUUGCUUGUGGGUCUUGUGCUGGUGGGUU
CUGUUAGCUCAGCGAAAUUCGAUGAGCUAUUUCAACCCGGCUGGGC
Protein
MVGMDLFKCVMMIMVLVVSCGEAVSGAKFDELYRSSWAMDHCVNEG
EVTKLKLDNYSGAGFESRSKYLFGKVSIQIKLVEGDSAGTVTAFYM
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Biological Data
Ø Descriptions
Ø Pictures
?
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Biological Data
Ø Descriptions
Ø Pictures
Ø Sequences
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Biological Data
Ø Descriptions
Ø Pictures
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
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Biological Data
Ø Descriptions
Ø Pictures
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
Ø Structures
A member of CGIAR c onsortium
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Biological Data
Ø Descriptions
Ø Pictures
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
Ø Structures
Ø Protein
Ø RNA
A member of CGIAR c onsortium
www.iita.org
Biological Data
Ø Descriptions
Ø Pictures
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
Ø Structures
Ø Protein
Ø RNA
Ø Interactions
A member of CGIAR c onsortium
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Biological Data
Ø Descriptions
Ø Pictures
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
Ø Structures
Ø Protein
Ø RNA
Ø Interactions
Ø Expressions
A member of CGIAR c onsortium
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Data Explosion
Ø Descriptions
Ø Pictures
Up to 600’000’000’000 (600GB) bases per experiment
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
Ø Structures
NGS
(Next Generation Sequencing)
Ø Protein
Ø RNA
Ø Interactions
Ø Expressions
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Up to 1 million data points per experiment
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Data Explosion
Ø Descriptions
Ø Pictures
Ø Sequences
Ø Protein
Ø RNA
Ø DNA
Ø Structures
Ø Protein
Ø RNA
Ø Interactions
Ø Expressions
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Data Analysis – DNA/RNA sequences
Sequence without knowledge connected to it is meaningless!
What to do?
Ø Sequence similarity
Ø Finding genes and regulatory elements
Ø Functional analysis of genes
Ø Homology
Ø Polymorphism
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Data Analysis
So we need bioinformatics tools and reference data
Hardware – Computing infrastructure (CPU, RAM, Storage)
Tools – Programs that process your data
Reference data – Databases for existing data
INTERNET– connection to external Databases
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Bioinformatics @ IITA
Hardware – Computing infrastructure (CPU, RAM, Storage)
HP Blade, with: Ø 3 blades with each 2 16-­core processors (AMD Opteron Processor 6272), Ø 384Gb RAM Ø 2Tb attached storage (DAS)
Ø 8TB attached storage (NAS)
The operating system is Ubuntu 14.04.1 LTS installed via biolinux 8.
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Data Analysis
So we need bioinformatics tools and reference data
Tools – Programs that process your data
Reference data – Databases for existing data
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Data Analysis – Data Format
FASTA
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Data Analysis – Data Format
GeneBank
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Data Analysis – Data Format
EMBL
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Data Analysis -­ Tools
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST, Needleman-­Wunsch, Smith-­Waterman
Ø Multi-­sequence alignment
Ø ClustalW, T-­coffee, Muscle Ø Sequence analysis
Ø EMBOSS, UGENE
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Data Analysis -­ Tools
Basic Local Alignment Search Tool
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST
http://blast.ncbi.nlm.nih.gov/Blast.cgi
http://www.ebi.ac.uk/ena/search/#Search
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Data Analysis -­ Tools
Basic Local Alignment Search Tool
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST
A member of CGIAR c onsortium
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Data Analysis -­ Tools
Basic Local Alignment Search Tool
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST
A member of CGIAR c onsortium
www.iita.org
Data Analysis -­ Tools
Basic Local Alignment Search Tool
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST
A member of CGIAR c onsortium
www.iita.org
Data Analysis -­ Tools
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST, Needleman-­Wunsch, Smith-­Waterman
Needleman-­Wunsch
Smith-­Waterman
A member of CGIAR c onsortium
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Data Analysis -­ Tools
ClustalW, T-­coffee, Muscle
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST, Needleman-­Wunsch, Smith-­Waterman
Ø Multi-­sequence alignment
Ø ClustalW, T-­coffee, Muscle
A member of CGIAR c onsortium
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Data Analysis -­ Tools
EMBOSS
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST, Needleman-­Wunsch, Smith-­Waterman
Ø Multi-­sequence alignment
Ø ClustalW, T-­coffee, Muscle Ø Sequence analysis
Ø EMBOSS
http://emboss.sourceforge.net/what/
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Data Analysis -­ Tools
UGENE
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST, Needleman-­Wunsch, Smith-­Waterman
Ø Multi-­sequence alignment
Ø ClustalW, T-­coffee, Muscle Ø Sequence analysis
Ø EMBOSS, UGENE
A member of CGIAR c onsortium
www.iita.org
Data Analysis -­ Tools
Ø Sequence similarity
Ø Pairwise-­sequence alignment
Ø BLAST, Needleman-­Wunsch, Smith-­Waterman
Ø Multi-­sequence alignment
Ø ClustalW, T-­coffee, Muscle Ø Sequence analysis
Ø EMBOSS, UGENE
A member of CGIAR c onsortium
www.iita.org
Data Analysis -­ Databases
Ø Sequence databases
Ø DNA
Ø EMBL -­ ENA – Ensembl
Ø NCBI – Entrez – GEO – UCSC
Ø DDBJ
Ø Pytozome
Ø Protein
Ø UniProt, SwissProt, Trembl
Ø RNA Ø Rfam, miRBase, Silva, Ø Pattern & Structure databases
Ø Annotation databases
Ø Diseases
Ø etc
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Data Analysis -­ Databases
Ø Sequence databases
Ø DNA
Ø EMBL -­ ENA – Ensembl
Ø NCBI – Entrez – GEO – UCSC
Ø DDBJ
http://www.ddbj.nig.ac.jp/
http://www.ncbi.nlm.nih.gov/nucleotide/
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http://www.ebi.ac.uk/ena
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Data Analysis -­ Databases
Ø Sequence databases
Ø DNA
Ø EMBL -­ ENA – Ensembl
Ø NCBI – Entrez – GEO – UCSC
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Data Analysis -­ Databases
Ø Sequence databases
Ø DNA
Ø NCBI – Entrez – GEO – UCSC
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Data Analysis -­ Databases
Ø Sequence databases
Ø DNA
Ø Ensembl (Plant)
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Data Analysis -­ Databases
Ø Sequence databases
Ø DNA
Ø Phytozome
A member of CGIAR c onsortium
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Data Analysis -­ Databases
Ø Sequence databases
Ø Protein
Ø UniProt, SwissProt, Trembl
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Data Analysis -­ Databases
Ø Sequence databases
RNA Ø Rfam, miRBase, Silva, A member of CGIAR c onsortium
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Bioinformatics
and this is only the …..
... enjoy bioinformatics!!
[email protected]
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