Workshop in Bioinformatics2009

Workshop in Bioinformatics2009

Class 2

Michal Linial Room A-515michall@cc.huji.ac.il

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