Workshop in Bioinformatics 2009
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Workshop in Bioinformatics 2009. Class 2. Michal Linial Room A-515 [email protected]. Workshop in Bioinformatics (2). Bioinformatics is the computer-assisted data management discipline : - PowerPoint PPT Presentation
Transcript of Workshop in Bioinformatics 2009
Workshop in Bioinformatics2009
Workshop in Bioinformatics2009
Class 2
Michal Linial Room [email protected]
Workshop in Bioinformatics (2)Workshop in Bioinformatics (2)
Bioinformatics is the computer-assisted data management discipline :
Gather, store, analyze, integrate biological and genetic information (data), and represent this information efficiently.
Bioinformatics - two facesBioinformatics - two faces
Analysis and interpretation of various types of data (sequences nt, aa, domains, signatures, structures, RNAs)
Development of new algorithms / statistics to assess biological information
Development and implementation of tools for access and management different types of information (DB, Models, Maps..)
What do you mean by “data”…
Raw (primary)
Processed (analyzed)
Integrated (systems)
What do you mean by “data”…
Raw (primary) Data Sequences
RNA DNA Genome
VariationsSNPMutations
DNA Sequencing
5’
5’ Primer
3’ TemplateG C A T G C
dATPdCTPdGTPdTTPddATP
dATPdCTPdGTPdTTPddCTP
dATPdCTPdGTPdTTPddTTP
dATPdCTPdGTPdTTPddGTPddGTP
GddC
GCATGddC
GCddA GCAddT ddG
GCATddG
“Classical” (Sanger)
ABI 3700 96x700 bases
G
C
T
A
+
_
+
_
G
C
A
T
G
C
short
long
capillary unit
New technology
“454” technology
(not in this class)
What do you mean data…
Raw (primary) Data Sequences
RNA DNA Genome
VariationsSNPMutations
Shotgun Sequencing
IsolateChromosome
ShearDNAinto Fragments
Clone intoSeq. Vectors Sequence
Shotgun Sequencing
SequenceChromatogram
Send to Computer AssembledSequence
Rat Sequencing
Deep Sequencing
New fast and cheap methods for sequencing
Replacing ? ‘classical’ Sanger sequencing
(not covered in this class but introduced later)
The main topicsThe main topicsIntroduction to databases
Working with sequences / Pairwise comparison
Database similarity searching
Profile building and searching
Functional resources
Genomics
Proteomics
Integrative resources
Introduction to systems biology
More…
The goal of the courseThe goal of the course
Introduction to variety of databases and tools Independence in working with available resources Critical evaluation of web tools Exposure to the main needs of modern biologist Leverage your research skills Discussing key issues in “new biology” Presenting front-line research projects based on BI
….but mainly fun
