workshop in bioinformatics 2010 class # 75321 class 8 march 2010
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Workshop in Bioinformatics2010
Class # 75321
Workshop in Bioinformatics2010
Class # 75321
Class 8 March 2010
(Molecular) Bioinformatics (Molecular) Bioinformatics
Development (Computational Biology)
New algorithms and statistics to assess biological information
Tools for access and management different types of information (DB, Models, Maps..)
User view (applied Bioinformatics)
Analysis: interpretation of various types of data (nt, aa, domains, RNAs, signatures, 3D-structures)
Statistical methods Applying predictions methods (from the shelf) Applying tools (web, programs…)
What do you mean “raw data”…
Raw (primary) Data Sequences
RNA (many types)DNA Genome
VariationsSNPMutationsCopy Number Variations (CNV)
What do you mean “raw data”…
Rate - Raw (primary) Data
HM1: Identify 2 areas with a similar (?) trend
The level of resolution:the ‘basic unit’ example DNA
Nucleotide to Genome level
NOTE: Not always the technology identify nucleotidein the DNA
HW2: provide an example…list the technology
The level of resolution:the ‘basic unit’ example DNA
Nucleotide to Genome level
Technology: DNA / RNA SEQUENCING
Nucleotide level
DNA Sequencing
“Classical” (Sanger)
5’
5’ Primer
3’ TemplateG C A T G C
dATPdCTPdGTPdTTPddATP
dATPdCTPdGTPdTTPddCTP
dATPdCTPdGTPdTTPddTTP
dATPdCTPdGTPdTTPddGTPddGTP
GddC
GCATGddC
GCddA GCAddT ddG
GCATddG
5’
5’ Primer
3’ TemplateG C A T G C
dATPdCTPdGTPdTTPddATP
dATPdCTPdGTPdTTPddATP
dATPdCTPdGTPdTTPddCTP
dATPdCTPdGTPdTTPddCTP
dATPdCTPdGTPdTTPddTTP
dATPdCTPdGTPdTTPddTTP
dATPdCTPdGTPdTTPddGTPddGTP
dATPdCTPdGTPdTTPddGTPddGTP
GddC
GCATGddC
GCddA GCAddT ddG
GCATddG
The level of resolution:the ‘basic unit’ example DNA
TECNOLOGY definitions:
Nucleotide (1)
Run (400-800) ABI –Sanger fluorescence capillary
Reads (35-400) SOLEXA and 454 (WGS) – BUT millions in parallel
ABI 3700 96x700 bases
Scale:capillary tech
RUNs
New technology
“454” technology
(not in this class)
G
C
T
A
+
_
+
_
G
C
A
T
G
C
short
long
G
C
T
A
+
_
+
_
G
C
A
T
G
C
short
long
The level of resolution:the ‘basic unit’ example DNA
FUNCTIONAL / Assembly definition (more)
SNP (1)
Indel (1-1000s) human genome -average 5 bp
EST (300-700)
Gene (1000 bacteria; 100,000 human; huge range)
Contig- 500,000, huge range / BacTig >106
Chromosome: Bacteria: 4*106, Human: 50- 250*106
Genome: HUGE ranges from virus 5*103 to frog 5*1010
Shotgun Sequencing
IsolateChromosome
ShearDNAinto Fragments
Clone intoSeq. Vectors:
PhagemidBAC
SequenceIsolate
ChromosomeShearDNA
into FragmentsClone into
Seq. Vectors:Phagemid
BAC
Sequence
1995-2006
SequenceChromatogram
Send to Computer AssembledSequence
SequenceChromatogram
Send to Computer AssembledSequence
Deep Sequencing
New fast and cheap methods for sequencing
Replacing ? ‘classical’ Sanger sequencing
(covered if time allows…)
The level of resolution:the ‘basic unit’ example DNA
Is genome is the “largest unit” ?
2008:
MetaGenomics
The BIOME project: A community of genomes in human body
SEARCH for numbers…
How many nucleotides in chromosome 7 of human….
1.Search “Google like”
2.Search “PubMED like”
3. Your way
HM3: the value, the source