Introduction to other
web-based resources
What? Where? and How? of
Bioinformatics
June 3, 2009
Bioinformatics
“Bioinformatics is the application of computer
technology to the management and analysis
of biological data. The result is that computers
are being used to gather, store, analyse and
merge biological data.”
(http://www.ebi.ac.uk/2can/bioinformatics/bioinf_what_1.html)
Protein seq
DNA seq
Protein
structure
Protein function
Applications
Real-life Bioinformatics
• Primary Data
– Gene or protein sequence
• GenBank/EMBL/DDBJ, UniProt
– Protein structure
• wwPDB
– Gene or protein interactions
• IntAct, DIP, BioGRID
– Functional studies
• PubMed
• Specialized databases (enzymes >> kinases)
• Secondary Data
– Protein families
• Pfam, Interpro
– Protein structure classifications
• SCOP, CATH
– Protein location, function
• GO
Where do we start?
Gene name &
synonyms
Micro-array
Data
Gene
expression
Disease/
SNP
Gene
sequence
Protein
interactions
Protein
sequence
Protein name &
synonyms
Protein
structure
Protein
function
Protein
domains
RCSB links
NCBI links
http://www.ncbi.nlm.nih.gov/Sitemap/index.html
http://www.ncbi.nlm.nih.gov/Education/index.html
NCBI bioinformatics tutorials
EBI links
http://www.ebi.ac.uk/
http://www.genome.jp/kegg/kegg2.html
KEGG links
Should I believe all I read/find?
• Source of information? (where/who)
– Scientific article?
– Web-based resource?
– Text book or other?
• Evidence for the conclusion? (how)
– Scientific experiment
– Electronic annotation
– Based on homology
• Sequence
• Modeling
– Hypothesis/generalization
How to read a scientific paper
•
•
•
•
•
Read Abstract
Read Introduction
Read Conclusion / Discussion
Read Methods
Review figures and figure legend
– Draw your own conclusion based on data
presented
– Do you agree with the author’s conclusion?
• Read results details
Searching for Lysozyme
• My name is Lysozyme. How well do you
know me?
Independently find all that you can about Lysozyme and make a report.