Bioinformatics

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• Bioinformatics
• BIO520/INF520
• Jim Lund

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Bioinformatics
Bioinformatics applies principles of information
science (derived from applied math, computer
science, and statistics) to make the vast,
diverse, and complex life sciences data more
understandable and useful. It automates simple
but repetitive types of analysis. Computational
biology uses mathematical and computational
approaches to address theoretical and
experimental questions in biology.
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Molecular information-DNA

• Raw bacterial DNA sequence
• Coding or not?
• Parse into genes?
• Find regulatory sequences?
• 4 bases ACGT
• 1kb for a gene
• Mb for a genome

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Genbank Growth
http//www.ncbi.nlm.nih.gov/Genbank/genbankstats.h
tml
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Protein Structure Determination
40,000 structures in 2006
10,000 structures in 2000
http//www.rcsb.org/pdb/static.do?pgeneral_inform
ation/pdb_statistics/index.html
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New Protein Folds
http//www.rcsb.org/pdb/static.do?pgeneral_inform
ation/pdb_statistics/index.html
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Protein Structure Prediction
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Transcript Analyses

• Northern Blot-1977

• Genomic transcript profiling

DeRisi, Iyer, Brown Science, 1998
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Proteomics
1978-1998
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Central Dogma of Molecular Biology
DNA
RNA
Protein
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Metabolic Networks
KEGG, 1998
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(No Transcript)
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Regulatory Networks
KEGG
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Bioinformatics-what is it?

• Acquisition, curation, and analysis of
• biological data

DATA
INFORMATION
KNOWLEDGE
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Bioinformatic Data-1978 to 2007

• DNA sequence
• Gene expression
• Protein expression
• Protein Structure
• Genome mapping

• Metabolic networks
• Regulatory networks
• Trait mapping
• Gene function analysis
• Scientific literature

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Goals of the HGP,1998-2003

• Reference Human Genome Sequence
• Draft 2001, Finish in 2003
• Improved Sequence Technology
• 0.25 per finished base
• Human Genome Sequence Variation
• Technology for Functional Genomics
• Comparative Genomics
• Finish Mouse by 2005 (well ahead here)
• ELSI
• Genome sequences highlight the finiteness of the
  set of sequences!

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What remains to be done?

• Comparative Genomics
• Description of mRNAs, proteins (identity and
  structure)
• Functional analyses
• Detailed understanding of development,
  regulation, variation

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The Gene for
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Other Reasons to Care
Affymetrix
Merck
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ELSI
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Bioinformatics and Genomics

• Biology major
• Pre-professionals
• Graduate Students
• Specialists
• Lab scientists
• Life Scientists
• Everyday uses
• Genomics
• Bioinformatics
• Public

• Computer Scientists
• Information Professionals
• Mathematicians
• Statisticians

HOW??
BIO520
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Life Scientist User Training

• WWW Watchout
• eg. Bizarre phylogenies
• Unread documentation
• Popular program sites with NO documentation
• Perhaps one day I will get around to writing some
  documentation-
• Help from a WWW service, hit several hundred
  times per day!

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Information ScienceDramatic Changes

• Information Storage
• Digital text, numbers, images
• Computerized Data Analysis
• Information Distribution
• WWW, e-mail, etc

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Moores Law
Intel Corporation
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Computer Science

• Operating Systems
• Programming
• Algorithms
• Not all problems solved
• Data structure/databases
• Interfaces
• Search and visualization

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BIO520 Nuts and Bolts

• Syllabus Schedule
• Textbook
• WWW
• Required Helpful
• Documentation

• Labs on Fridays
• In NURS 602J 2-4pm
• Exams (2 final)

http//elegans.uky.edu/520
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BIO520 Topics

• Navigating biological databases.
• DNA sequence
• Gene structure and function
• Proteins
• - 3D structure, motif analysis
• Phylogenetic inference
• Genome/transcriptome/proteome
• Function Analyses
• Computer how-tos

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Textbooks

• Bioinformatics A Practical Guide to the Analysis
  of Genes and Proteins, 3rd Ed.
• Baxevanis and Ouellette
• Biology background material
• Genes VIII (Lewin)
• Cell Biology (Watson et al, Darnell et al)
• NCBI Bookshelf (http//www.ncbi.nlm.nih.gov/entrez
  /query.fcgi?dbBooksitooltoolbar)

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Computer Resources

• http//elegans.uky.edu/520
• e-mail
• listserv BIO520_at_lsv.uky.edu
• Programs
• VectorNTI
• RasMol, Cn3D, Clustal
• Web based resources
• Databases
• Software programs

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Biological Principles

• Evolution by natural selection
• DNA-gtRNA-gtProtein
• Structure?Function