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Bio(-)informatics
Bio = Biology/biological
What is Bioinformatics?
Mathematical, statistical and
computing methods that aim to solve
biological problems using DNA and
amino acid sequences and related
information.
Bioinformatics is conceptualizing biology in terms
of macromolecules and then applying
“informatics” techniques to understand and
organize the information associated with these
molecules, on a large scale.
CCS HAU Bioinformatics
Bioinformatics
• Bioinformatics is the application of
information technology to analyze, process,
and manage biological data.
Overview
• Biological databases are being produced at a phenomenal
rate
• As a result computers are becoming indispensable for
biological research
• Aims
1- organize data
2- develop tools
3- use tools to apply to biology
CCS HAU Bioinformatics
Definitions:
Biocomputing and computational biology are synonyms and
describe the use of computers and computational techniques to
analyze any type of a biological system, from individual molecules
to organisms to overall ecology.
Bioinformatics describes using computational techniques to
access, analyze, and interpret the biological information in any
type of biological database.
Sequence analysis is the study of molecular sequence data for
the purpose of inferring the function, interactions, evolution, and
perhaps structure of biological molecules.
Genomics analyzes the context of genes or complete genomes
(the total DNA content of an organism) within the same and/or
across different genomes.
Proteomics is the subdivision of genomics concerned with
analyzing the complete protein complement, i.e. the proteome, of
organisms, both within and between different organisms.
CCS HAU Bioinformatics
Rate of growth
CCS HAU Bioinformatics
The Promises
• Digitization of the biological systems and
processes
Simulation and Modeling of protein-protein
interactions, protein pathways, genetic networks,
biochemical and cellular processes, normal and
disease physiological states,…
• Blurring of the boundary between
experimentally generated data and
computational data search and analysis
• In silico discovery in complement with
wet lab experiments
The Landscape of Biological Data Sources
PRINTS Patent USPTO
BLOCKS PFAMB
PIR GENEPEPT
PFAMA Patent PCT
NUCLEOTIDE REPOSITORY
• EMBL- European Molecular Biology Laboratory, at Cambridge, UK.
• GENBANK- at NCBI, a division at NIH campus, USA.
• DDBJ- DNA Data Bank of Japan, Mishima, Japan
NCBI
EMBL
ClustalW
Microarray Data Integration
Integration (FASTA)
(RDBMS, Excel) BioInformatics
BioInformatics
Examples of Bioinformatics
• Database interfaces
– Genbank/EMBL/DDBJ, Medline, SwissProt, PDB, …
• Sequence alignment
– BLAST, FASTA
• Multiple sequence alignment
– Clustal, MultAlin, DiAlign
• Gene finding
– Genscan, GenomeScan, GeneMark, GRAIL
• Protein Domain analysis and identification
– pfam, BLOCKS, ProDom,
• Pattern Identification/Characterization
– Gibbs Sampler, AlignACE, MEME
• Protein Folding prediction
– PredictProtein, SwissModeler
CCS HAU Bioinformatics
Five websites that all biologists should
know
• NCBI (The National Center for Biotechnology Information;
– http://www.ncbi.nlm.nih.gov/
• EBI (The European Bioinformatics Institute)
– http://www.ebi.ac.uk/
• The Canadian Bioinformatics Resource
– http://www.cbr.nrc.ca/
• SwissProt/ExPASy (Swiss Bioinformatics Resource)
– http://expasy.cbr.nrc.ca/sprot/
• PDB (The Protein Databank)
– http://www.rcsb.org/PDB/
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CCS HAU Bioinformatics
CCS HAU Bioinformatics
Challenges in bioinformatics
• Explosion of information
– Need for faster, automated analysis to process large
amounts of data
– Need for integration between different types of
information (sequences, literature, annotations, protein
levels, RNA levels etc…)
– Need for “smarter” software to identify interesting
relationships in very large data sets
• Lack of “bioinformaticians”
– Software needs to be easier to access, use and
understand
– Biologists need to learn about the software, its
limitations, and how to interpret its results
CCS HAU Bioinformatics
Your Turn:
ANY Question(s)