Introduction to Bioinformatics Bioinformatics Tools

1
Introduction to Bioinformatics Bioinformatics
Tools Databases

• COIN81 - Spring 2009
• Foothill College

2
COIN81 Overview

• Hands on course (Internet delivery)
• Bioinformatics Web resources
• Internet literacy in bioinformatics
• Bioinformatics tools and databases
• Sequence, structure, function theme
• Multiple venues
• Online course Spring 2009
• Casual lectures TBA (KCI)

3
Course Introduction

• What is bioinformatics?
• Molecular biology review
• Web technologies review
• NCBI tour (two-part lecture)
• Required reading
• Commercialization of Bioinformatics
• Molecular Genetics Primer (DOE)

4
Introduction to NCBI

• NCBI mission
• NCBI resources
• NCBI tour
• BLAST search
• GenBank / NCBI data model
• LocusLink / NCBI databases
• Retrovirus / genome resources

5
(No Transcript)
6
PubMed / Medline

• Electronic texts
• Scientific and medical
• Housed at NCBI
• Usually abstracts only
• Links to pay-per-view scientific articles
• Great background information
• Helpful for finding peer reviewed data

7
BLAST

• BLAST home
• BLAST tour
• BLAST tutorials
• BLAST demo
• BLAST exercises

8
(No Transcript)
9
GenBank, EMBL, DDBJ

• GenBank
• Data model and resources
• Genome, proteome, and GenPept
• EMBL
• Specific resources
• XML initiative http//www.ebi.ac.uk/xembl/
• DDBJ
• DNA Data Bank of Japan
• Japanese genomic projects

10
NCBI Data Model

• Genome and Proteome
• Accession number entry
• References / citations
• Includes direct submission
• Full sequence data / contigs
• Post translational modifications
• SNP / expression references

11
NCBI Gene

• Gene as the center of NCBI
• Links to all of NCBI databases
• Guide to gene locations
• Map Viewer for navigation
• Excellent visual guide
• Links to HomoloGene / UniGene
• SNP and expression data also linked

12
(No Transcript)
13
NCBI Resources
14
UniProt

• UniProt (Universal Protein Resource) is the
  world's most comprehensive catalog of information
  on proteins
• Swiss-Prot / TrEMBL / PIR resources
• References / citations
• Sequence data for protein
• PDB and structure links
• Links to GenBank entries

15
(No Transcript)
16
PROSITE - Database of Protein Families and
Domains
17
Structure Analysis
18
Protein Data Bank

• Protein Data Bank
• Archive of .pdb files
• Structures determined by X-ray, NMR
• Theoretical Structure Search
• Features a Molecule of the Month
• Links to SWISS-MODEL
• First approach calculations
• Rapid homology search / sort
• http//www.rcsb.org/pdb/

19
(No Transcript)
20
PIR

• Protein Information Resource
• iProClass and PRI-NREF
• PIR-PSD, Swiss-Prot, TrEMBL, RefSeq, GenPept,
  and PDB
• http//pir.georgetown.edu/
• Integrated public resource of protein informatics
• Supports genomic and proteomic research and
  scientific discovery - iProClass and PRI-NREF

21
(No Transcript)
22
Pfam

• Protein family and domains
• View protein domain architectures
• Conserved domains
• These appear in NCBI BLASTp
• Follow links into COGs and Pfam
• Great functional data
• What does the domain do?
• Links to structure data
• Download models of domain / protein

23
(No Transcript)
24
Biology Workbench

• Web front end to SDSC
• San Diego Super Computer
• Nucleic tools, protein tools, structure tools
• Run bioinformatics tools against your sequences,
  compare to other databases
• We will do phylogenetic comparisons
• HIV mutation, Prions, and SARS exercises
• Super Computer power on a Web browser budget
  all available through the Internet!

25
(No Transcript)
26
Dendrogram for HIV SIV HTLV STLV
27
Genome Resources

• Mouse genome
• Yeast genome
• Retroviruses
• HIV, SIV
• HTLV, STLV
• Herpes
• E.coli
• Human genome

28
GeneCards

• GeneCards is a database of human genes, their
  products and their involvement in diseases. It
  offers concise information about the functions of
  all human genes that have an approved symbol, as
  well as selected others.
• http//bioinfo.weizmann.ac.il/cards/

29
(No Transcript)
30
GeneLynx

• GeneLynx http//www.genelynx.org/
• A Portal to the Human Genome
• GeneLynx is a portal to a collection of
  hyperlinks for each human gene. It is implemented
  as an easily extensible relational database with
  a straightforward user interface (definitions
  too!)
• If you had to have one point of entry for linking
  to all of the Web databases for a gene this is
  it!

31
(No Transcript)
32
Ensembl Genome Browser

• Ensembl is a joint project between EMBL - EBI and
  the Sanger Institute to develop a software system
  which produces and maintains automatic annotation
  on eukaryotic genomes.
• Ensembl presents up-to-date sequence data and the
  best possible automatic annotation for metazoan
  genomes.
• http//www.ensemble.org/

33
(No Transcript)
34
Stanford Microarray Database

• SMD stores raw and normalized data from
  microarray experiments, as well as their
  corresponding image files.
• In addition, SMD provides interfaces for data
  retrieval, analysis and visualization.
• Data is released to the public at the
  researcher's discretion or upon publication.
• http//genome-www5.stanford.edu/

35
(No Transcript)
36
Contact Information

• Robert D. Cormia
• Foothill College - CTIS Division
• Room 4129
• 650.949.7456
• rdcormia_at_earthlink.net
• http//www.informaticus.org/COIN81/
• 650.747.1588