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Central Dogma
Information storage in molecules
replication
DNA
transcription
RNA
translation
Protein
Proteins
Carbon-Nitrogen backbone
amino acid side chains
The twenty amino acids
Translation:
RNA
Proteins
How do we get from bases to amino acids?
1nt => 1aa can code for 4 aa
2nt => 1aa can code for (4x4)= 16 aa
3nt => 1aa can code for (4X4x4)= 64 aa
The code consists of continuous Nonoverlapping triplets
GCA CCC GCG AAG
Ala Pro Ala
Lys
G CAC CCG CGA AG
His Pro Arg
The genetic code is:
Degenerate-most amino acids have
more than one code
word
often these redundant
codes share the same
first two bases
The genetic code: another view
Codons in the
same color
encode
identical amino
acids
What are the likely effects of a mutation at the first vs.
third codon position?
The Genetic code is universal (mostly)
some exceptions-
eg-Mycoplasma TGA=Trp (instead of stop)
Candida cylindrica CTG= Ser (instead of Leu)
mitochondrial DNA—several different exceptions depending on organism
NCBI site covering alternative genetic codes:
http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
The Codon Usage Database
http://www.kazusa.or.jp/codon/
Leading vs lagging strand synthesis
%G+C content
plotted as difference from
genomic mean
GC skew = (G-C)/(G+C)
Theoretical range from -1 to 1
An indication of origin of replication
Prochlorococcus MED4
Prochlorococcus MIT9313
Genome %G+C=31%
Genome %G+C=51%
Genetic code
61 possible codons
(64-3 stop)
BUT, not all are used
with equal frequency
Measures of codon usage

Measures based on a set of highly expressed
genes (presumed optimal CU)
 CAI
(codon adaptation index)
 Fop (Frequency of optimal codons)
 CBI (codon bias index)

Measures independent of presumed optimal
codon set
 Nc
(effective number of codons)
 RFSCU (Relative frequency of synonymous codon
usage)

Read more about these at
 http://www.molbiol.ox.ac.uk/cu/Indices.html
Role of tRNA complement in
translation efficiency
1 tRNA recognizes a particular codon
BUT, most genomes do not have 61 tRNA genes……
Getting Artemis

Go to Sanger center web site
 Software/Informatics/artemis

Download Artemis V8
 Save

in Ocean 539D folder
Make a shortcut to the .jar file on the
desktop
 Edit
the properties of the shortcut and add
"java -mx250m -jar " to the start of the Target:
field.
0
0.
36
0.
33
0.
29
0.
26
0.
22
0.
19
0.
16
0.
50
100
63
200
0.
46
300
59
400
0.
43
500
55
MED4
0.
39
%G+C
51
47
43
39
35
31
25
Frequency
#of genes
MED4
200
150
100
50
0
Effective number of codons (Nc)