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Bioinformatics for biomedicine Seminar: Sequence analysis of a favourite gene Lecture 5, 2006-10-17 Per Kraulis http://biomedicum.ut.ee/~kraulis What is bioinformatics? Basic databases and tools Sequence searches: BLAST, FASTA Multiple alignments, phylogenetic trees

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bioinformatics for biomedicine seminar sequence analysis of a favourite gene

Bioinformatics for biomedicineSeminar: Sequence analysis of a favourite gene

Lecture 5, 2006-10-17

Per Kraulis

http://biomedicum.ut.ee/~kraulis

course design
What is bioinformatics? Basic databases and tools

Sequence searches: BLAST, FASTA

Multiple alignments, phylogenetic trees

Protein domains and 3D structure

Seminar: Sequence analysis of a favourite gene

Gene expression data, methods of analysis

Gene and protein annotation, Gene Ontology, pathways

Seminar: Further analysis of a favourite gene

Course design
from the previous lecture
From the previous lecture
  • 3D structure
    • Relation to function
    • Methods of determination
    • Databases
  • Domains
    • Definition
    • Relation to function
    • Databases
3d structure and sequence 1
3D structure and sequence, 1
  • Sequence determines structure
  • Anfinsen’s experiments: folding
  • 3D structure prediction should work!
    • First principles (physics)
      • Extremely difficult
      • Only special cases
    • By similarity
      • Works reasonably
      • Depends on many factors
3d structure and sequence 2
3D structure and sequence, 2
  • Similar sequence -> similar structure
    • General statement
    • No “real” counterexamples
      • But a designed, extreme case exists
  • A single 3D structure represents a family
    • Depending on sequence similarity
  • Many sequences “allowed” for a structure
3d structure and sequence 3
3D structure and sequence, 3
  • Many sequences “allowed” for a structure
    • Sequence divergence possible over time
  • Structure more conserved that sequence
    • Sequence may diverge beyond recognition
    • Structure may still be similar
    • Apparently unrelated sequences may form similar structures!
3d structure and sequence 5
3D structure and sequence, 5
  • Protein design
    • Target: A given structure
    • Specify a sequence that folds into it
  • Some success in recent years
    • First principles approach
      • Computational prediction
    • Evolutionary approach
      • In vitro evolution experiments
3d structure and sequence 4
3D structure and sequence, 4
  • Example: TIM barrel
    • TIM = Triose isomerase
    • Example in PDB: 1TRI
    • Symmetrical, 8 alpha-beta units
    • Enzymes
      • Wide range of reactions, substrates
  • Some TIM barrels have no significant sequence similarity
    • Sequence divergence?
    • Structure convergence?
structure database
Structure database
  • PDB database
    • At RCSB: http://www.rcsb.org/pdb/
    • Via UniProt: http://www.ebi.uniprot.org/
  • Many different 3D viewers
    • KiNG (uses Java)
    • RasMol (requires installation)
unknown sequence
Unknown sequence?
  • Given unknown sequence, what to do?
    • Set up a check list
      • Never optimal
  • Note: Unrealistic exercise
    • “Premier tool of analytic chemistry: the phone”
    • Consider known facts before analysis
    • Consider the underlying problem
check list outline
Check list, outline
  • Where to search first?
    • UniProt
    • Pfam
    • Ensembl
  • Function?
    • Annotation
    • Similarities
    • Domains, structure
slide12
Unk1
  • File “unk1-seq.txt”
  • Human protein
  • No other info
unk1 caspase 8
Unk1 = Caspase 8
  • Protease
    • Cysteine peptidase C14
    • Cascade, activation of others
  • Hormone-triggered
    • TNF (tumor necrosis factor)
  • Multicellular organisms
    • Apoptosis (programmed cell death)
    • Development, cancer
slide14
Unk2
  • File “unk2-seq.txt”
  • From C. elegans
    • Result of genetic screen
  • Orthologue in human?
unk2 nhr 25
Unk2 = nhr-25
  • Nuclear receptor (NR) family
    • Transcription factor
    • DNA-binding domain
    • Hormone-receptor domain
  • Orphan NR
    • Unknown ligand; maybe none
  • Multicellular organisms
    • Developmental processes
      • Moulting in insects
slide16
Unk3
  • File “unk3-seq.txt”
  • Mouse protein
  • No other info
unk3 gpr141
Unk3 = GPR141
  • GPCR
    • G-protein coupled receptor
    • 7TM, seven transmembrane helices
  • Orphan GPCR
    • Unknown ligand
  • Human ortholog, Ensembl search
    • http://www.ensembl.org/Multi/blastview/BLA_4CBTgZfhK
task for this week
Task for this week
  • Perform analysis of sequences
    • http://biomedicum.ut.ee/~kraulis/bioinfo_biomed/
    • unk4-seq.txt (Danio rerio, zebrafish)
    • unk5-seq.txt (human, fragment)
  • Organism?
  • Protein family?
  • Structure and function?
  • Human medical relevance?