Workshop in Bioinformatics - TeachLine

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2 Οκτ 2013 (πριν από 4 χρόνια και 3 μήνες)

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Workshop in Bioinformatics

2009

Class 2



Michal Linial Room A
-
515

michall@cc.huji.ac.il

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 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

Variations


SNP


Mutations



DNA Sequencing

5’

5’ Primer

3’ Template

G C A T G C

dATP

dCTP

dGTP

dTTP

ddATP

dATP

dCTP

dGTP

dTTP

ddCTP

dATP

dCTP

dGTP

dTTP

ddTTP

dATP

dCTP

dGTP

dTTP

ddGTP

G
ddC

GCATG
ddC


GC
ddA


GCA
ddT


ddG

GCAT
ddG


“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

Variations


SNP


Mutations


Shotgun Sequencing

Isolate

Chromosome

ShearDNA

into Fragments

Clone into

Seq. Vectors

Sequence

Shotgun Sequencing

Sequence

Chromatogram

Send to Computer

Assembled

Sequence

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 topics

Introduction 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 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