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What is Bioinformatics?
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How to find me
DD2396 Bioinformatics
Lars Arvestad
Address: Roslagstullsbacken 35
Albanova
Phone:
5537 8565
Email:
[email protected]
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What is Bioinformatics?
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What is Bioinformatics?
What is Bioinformatics?
• Bioinformatics 6= sequence analysis
There is:
• Automatic analysis of literature
• Analysis of gene expression
• Proteins as molecules, not sequences
• Interactions between gene and/or
proteins
• Modeling the cell
”In silico biology”, computational biology
Refinement of lab results
Reduction of wet-lab work by computational
predictions:
• ”Which gene could cause this?”
• ”What 3D structure does this protein have?”
• Structuring and handling of datasets in
molecular biology
Structure: ”What is a gene? How do we store
its information?”
• Infrastructure: ”How can researchers access
this data?”
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What is Bioinformatics?
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What it is not
My take:
• Extracting knowledge from biomolecular
data
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What is Bioinformatics?
Central theme : Methods
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Course goals
• Understand possibilities and limitations with
Bioinformatics
• Be able to use lab-supporting
Method = Algorithm + Data + Art
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What is not in the course
Bioinformatics in the industry.
• Work in a lab and use Bioinformatics for
analyzing results.
• Prepare for PhD studies
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What is Bioinformatics?
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Databases
In general
• Is this a novel gene?
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Wet lab
Biophysics
Statistics (well, a little bit)
No programming
• I have a novel protein. What structure does
it have?
• What genes are found in platypus?
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Example: Wood genes and frogs
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Basic idea for Swedish Human Proteome
Resource:
• In what tissues are proteins/genes active?
Where in the cell?
• Consider all known human genes, choose
peptides
• Generate antibodies for selected peptides
• Stain tissues with antibodies
• Study, annotate, and store in database
Henrik Aspeborg, KTH:
• Found new gene in hybrid aspen
• Very active during wood formation
• 60 aa strongly similar to a pattern first found
in frog. Function: localizes to microtubuli
• Contains typical phosphorelation sites
What is Bioinformatics?
Application examples
Example: Lab support for HPR
Goal: How do you synthesize cellulose?
• Sequence genes active during wood
formation
• Compare with known genes: What’s new?
• Look for interesting properties
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What is Bioinformatics?
Example: Lab support for HPR
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Evolution of HIV
Bioinformatics: How choose peptides?
Constraints:
• What genes?
• Avoid membrane bound proteins!
• Select unique peptides!
Leitner and Albert, 1995
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What is Bioinformatics?
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What is Bioinformatics?
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Requirements
Course web: http://www.csc.kth.se/
DD2396/bioinfh09
Schedule: KTH web.
Lecture contents on the course page!
Registration: Link to form on course web
Lecturer: Me!
Assistants: Hossein Farahani, Joel Sjöstrand
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Computer labs
• Four scheduled lab times
• Three main assignment sets
• Present your results in lab (no report)
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3 computer labs
Exam
What is Bioinformatics?
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Home assignments
• 4 home assignments distributed.
• Deadlines to be determined.
• Approved solutions give points towards first
part of exam.
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Optional extra assignments
• Part 1: ”theory”
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• Part 2: ”practice”
1 optional project
”Lab 4”, requires written report.
Bumps your grade one step!
• About 15 points each
• 15 points for passing grade
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• Bonus only applicable on part 1
1 optional essay
Bumps your grade one step!
• Part 2 not graded if part 1 has less than 10
points
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Litterature
What is Bioinformatics?
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Hundreds, each with different angle!
• Proteins
• Genes
• Genomes
• Certain gene familes (GPCRs, TF)
• Gene expression
• Interactions
• Pathways
• Evolutionary histories
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Sequence databases
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Application examples
Bioinformatics database
Book: Zvelebil and Baum, Understanding
Bioinformatics.
Lab notes: Buy at CSC student office, Osquars
Backe 2.
Extras: See course home page
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What is Bioinformatics?
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In the beginning
Primary and secondary
Annotated and automatic
”Hobby collections” vs industrial
projects
Margaret Oakley Dayhoff:
Atlas of Protein Sequences
60’s: A book on protein sequences
1972: Electronic distribution
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What is Bioinformatics?
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Swiss-Prot
• Based on Atlas
• 1986: 3 900 sequences
• 2007: 252 616 sequences
• 2009: 405 506 sequences
• Curated database
• Part of UniProt consortium
Databases
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Example: Hemoglobin A
Sequence data in Fasta format
id
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ion
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>Q3MIF5|Q3MIF5_HUMAN Hemoglobin, alpha 1 - Homo sapiens
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS
HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFK
LLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
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Common problems with sequences
databases
What is Bioinformatics?
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UniProt: foremost protein DB
• www.uniprot.org
• Redundancy:
• Different sources (genome projects, directed
sequencing)
• ”Posttranslational editing”
• Exactly the same protein, different species
• Actual manual errors:
• bad annotetion
• bad sequencing
• bad scientist!
• Automatic annotation — dangerous
• ”Hemoglobin, alpha 1” in a plant?
• Better? ”Similar to Q3MIF5_HUMAN
Hemoglobin, alpha 1 - Homo sapiens”
• ”Hypothetical protein”
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What is Bioinformatics?
• International collaboration
• Stores
• sequence data
• ”non-redundant” data sets
• cross references to other DB’s
• literature references
• annotation about function etc.
• Powerful search methods
• User friendly
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PDB: Protein Data Bank
What is Bioinformatics?
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Nucleotide databases
• www.pdb.org
structure
• Today: 55 271
structures
• Structure details,
sequence data,
weight, known
function, litterature,
chemical and
biological knowledge
• Pretty pictures!
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What is Bioinformatics?
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Genome analysis at Ensembl
• www.ensembl.org
• Stores, analyses, and presents chosen
Eukaryotic genomes
• User friendly, yet advanced
• You find
• gene and protein sets
• species comparisons
• data on genomic variation
• (not the best user interface)
Application examples
• Source for refined collections
Hutchison,
Nucl Acid Res 2007
• Hosting
• GenBank, ”nr”, ”nt”, etc
• PubMed
• genome project
• taxonomy knowledge
• and more
What is Bioinformatics?
• Journals require deposition
Hemoglobin A
NCBI
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• Hub for data gathering
GenBank
EMBL
DDBJ
• Molecules with solved
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Zoom from chromosome...
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...down to gene
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Gene for hemoglobin A
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Summary
• Many different sources: Search actively for
data!
• Some source are vital: Your first attempt
• Do not trust data!
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What is Bioinformatics?
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Next time
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Comparing sequences
Visualizing similarity
Alignments
Scoring systems
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