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Contact What is Bioinformatics? Application examples This course Databases End Contact What is Bioinformatics? Application examples This course Databases End Databases End How to find me DD2396 Bioinformatics Lars Arvestad Address: Roslagstullsbacken 35 Albanova Phone: 5537 8565 Email: arve@csc.kth.se Contact What is Bioinformatics? Application examples This course Databases End Contact 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?” • Contact What is Bioinformatics? Application examples This course Databases This course What it is not My take: • Extracting knowledge from biomolecular data • • • Application examples End Contact What is Bioinformatics? Central theme : Methods Application examples This course Databases End Course goals • Understand possibilities and limitations with Bioinformatics • Be able to use lab-supporting Method = Algorithm + Data + Art Contact What is Bioinformatics? Application examples This course Databases What is not in the course Bioinformatics in the industry. • Work in a lab and use Bioinformatics for analyzing results. • Prepare for PhD studies End Contact What is Bioinformatics? Application examples This course Databases In general • Is this a novel gene? • • • • 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? End Contact What is Bioinformatics? Application examples This course Databases End Contact Example: Wood genes and frogs Application examples This course Databases This course Databases End 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 Contact What is Bioinformatics? End Contact What is Bioinformatics? Example: Lab support for HPR Application examples This course Databases End Databases End Databases End Evolution of HIV Bioinformatics: How choose peptides? Constraints: • What genes? • Avoid membrane bound proteins! • Select unique peptides! Leitner and Albert, 1995 Contact What is Bioinformatics? Application examples This course Databases End Contact What is Bioinformatics? This course What is Bioinformatics? Application examples This course This course 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 Contact Application examples Databases Computer labs • Four scheduled lab times • Three main assignment sets • Present your results in lab (no report) • • End Contact 3 computer labs Exam What is Bioinformatics? Application examples This course Home assignments • 4 home assignments distributed. • Deadlines to be determined. • Approved solutions give points towards first part of exam. Contact What is Bioinformatics? Application examples This course Databases End Contact What is Bioinformatics? Exam Application examples This course Databases End Optional extra assignments • Part 1: ”theory” • • 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 • • 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 Contact What is Bioinformatics? Application examples This course Databases End Contact Litterature What is Bioinformatics? Application examples • • This course Databases End Hundreds, each with different angle! • Proteins • Genes • Genomes • Certain gene familes (GPCRs, TF) • Gene expression • Interactions • Pathways • Evolutionary histories This course Databases End Contact Sequence databases • 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 Contact What is Bioinformatics? What is Bioinformatics? Application examples This course Databases End Databases End 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 Contact What is Bioinformatics? Application examples This course Swiss-Prot • Based on Atlas • 1986: 3 900 sequences • 2007: 252 616 sequences • 2009: 405 506 sequences • Curated database • Part of UniProt consortium Databases End Contact What is Bioinformatics? Application examples This course Example: Hemoglobin A Sequence data in Fasta format id que i n ”, u ion s r s ke ce Mar ”Ac ive ript c s e es d m i t e n som atio , t e o Nam Ann >Q3MIF5|Q3MIF5_HUMAN Hemoglobin, alpha 1 - Homo sapiens MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFK LLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR Contact What is Bioinformatics? Application examples This course Databases End Contact Common problems with sequences databases What is Bioinformatics? Application examples This course Databases Application examples This course Databases End 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” Contact 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 End Contact PDB: Protein Data Bank What is Bioinformatics? Application examples This course Databases End Nucleotide databases • www.pdb.org structure • Today: 55 271 structures • Structure details, sequence data, weight, known function, litterature, chemical and biological knowledge • Pretty pictures! Contact What is Bioinformatics? Application examples This course Databases End Contact What is Bioinformatics? Application examples This course Databases End 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 Contact • Hub for data gathering GenBank EMBL DDBJ • Molecules with solved This course Databases Zoom from chromosome... End Contact What is Bioinformatics? Application examples This course ...down to gene Databases End Contact What is Bioinformatics? Application examples This course Databases End Gene for hemoglobin A Contact What is Bioinformatics? Application examples This course Databases Summary • Many different sources: Search actively for data! • Some source are vital: Your first attempt • Do not trust data! Contact What is Bioinformatics? Application examples Next time • • • • Comparing sequences Visualizing similarity Alignments Scoring systems This course Databases End End
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