Bioe131: Introduction to Computational Biology

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Bioe131 Introduction to Computational Biology
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Molecular Biology Primer
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strong
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(Some ribosomes are free-floating in the cytosol)
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Also localization, degradation, sequestration,
NMD, RNAi,
(depending on organism)
Exon Junction Complex (triggers Nonsense-Mediated
Decay if not removed by ribosome)
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Amino acids
Usually found as a zwitterion
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RNA structure
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Biological Databases
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Chemical structures -omics experimental data
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Relational databases

• Relational database theory (E.F.Codd, 1970)
• Data stored as a collection of tables
• Relational operators specify links between
  tables
• Structured Query Language (SQL) for accessing
  data
• RDBMS Relational Database Management System
• Unfortunately
• Much bioinformatics infrastructure predates
  RDBMSs
• Lots of biological data stored in flatfiles
• File formats idiosyncratic (not systematic like
  e.g. XML)

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Querying sequence databases

• I think these two proteins are related
  (homologous). Whats the nature of their
  relationship?
• Method pairwise sequence alignment
• I have just sequenced a protein. What proteins
  in SwissProt are most similar?
• Method homology search

Alignment homology search are closely related
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http//www.rcsb.org/pdb
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(BLOCKS, Pfam, SMART, InterPro, PhyloFacts)
MULTIPLE SEQUENCE ALIGNMENTS
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Genome annotation databases
GFF, etc.
UCSC Browser genome.ucsc.edu
GBrowse www.gmod.org Flybase flybase.net/annot
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Ontologies

• Biological knowledge is rife with terminological
  ambiguity
• Protein synthesis
• Translation
• Gene expression
• Two (broad) approaches
• Bottom-up attempt to use Natural Language
  Processing techniques to find clusters of terms
  in the literature
• Top-down attempt to systematize the
  representation of scientific knowledge using
  formal ontologies
• E.g. http//www.geneontology.org/

Do these mean the same thing, or not?
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Pathway databases Reactome

• E.g. Reactome

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Pathway databases EcoCyc
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Pathway databases WikiPathways
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CellML model repository