Title: Bioinformatics
1- Bioinformatics
- BIO520/INF520
- Jim Lund
2Bioinformatics
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.
3Molecular 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
4Genbank Growth
http//www.ncbi.nlm.nih.gov/Genbank/genbankstats.h
tml
5Protein 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
6New Protein Folds
http//www.rcsb.org/pdb/static.do?pgeneral_inform
ation/pdb_statistics/index.html
7Protein Structure Prediction
8Transcript Analyses
- Genomic transcript profiling
DeRisi, Iyer, Brown Science, 1998
9Proteomics
1978-1998
10Central Dogma of Molecular Biology
DNA
RNA
Protein
11Metabolic Networks
KEGG, 1998
12(No Transcript)
13Regulatory Networks
KEGG
14Bioinformatics-what is it?
- Acquisition, curation, and analysis of
- biological data
DATA
INFORMATION
KNOWLEDGE
15Bioinformatic 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
16Goals 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!
17What remains to be done?
- Comparative Genomics
- Description of mRNAs, proteins (identity and
structure) - Functional analyses
- Detailed understanding of development,
regulation, variation
18The Gene for
19Other Reasons to Care
Affymetrix
Merck
20ELSI
21Bioinformatics 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
22Life 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!
23Information ScienceDramatic Changes
- Information Storage
- Digital text, numbers, images
- Computerized Data Analysis
- Information Distribution
- WWW, e-mail, etc
24Moores Law
Intel Corporation
25Computer Science
- Operating Systems
- Programming
- Algorithms
- Not all problems solved
- Data structure/databases
- Interfaces
- Search and visualization
26BIO520 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
27BIO520 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
28Textbooks
- 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)
29Computer 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
30Biological Principles
- Evolution by natural selection
- DNA-gtRNA-gtProtein
- Structure?Function