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3. genome analysis
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The first DNA-based genome to be sequenced in its
entirety was that of bacteriophage Φ-X174; (5,368 bp),
sequenced by Frederick Sanger in 1976
3. genome analysis
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The first DNA-based genome to be sequenced in its
entirety was that of bacteriophage Φ-X174; (5,368 bp),
sequenced by Frederick Sanger in 1976
There are several things to notice in this plot. First, the genome is
circular. The density of the four nucleotides are plotted in the
four outer-most circles. This density is not evenly distributed;
although all four of the scales range from 0% (min., no colour) to
40% (max colour intensity), it can be easily seen that the sequence
is dominated by T's (red circle), and that there are relatively few
G's (outermost turquoise circle) and C's (pink circle), and a few Arich regions (green 2nd circle). There are many genes which
overlap (the genes are indicated in the "annotation circle", which is
the fifth circle from the outside - with the blue bands
representing genes in the forward direction).
GC Skew = (G - C)/(G + C)
AT Skew = (A - T)/(A + T)
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/PhiX.html
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exploring
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exploring
genomes
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exploring
genomes
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Circular maps of the chromosome and plasmids of enteropathogenic E. coli
(da Iguchi A et al. J. Bacteriol. 2009)
CDS = CoDing Sequence, region of nucleotides that corresponds to
the sequence of amino acids in the predicted protein
PP = prophage: a phage (viral) genome inserted
and integrated into the circular bacterial DNA
chromosome
IE = integrative elements
Circular maps of the chromosome and plasmids of EPEC strain E2348/69. (A) EPEC strain E2348/69 chromosome. From the outside
in, the first circle shows the locations of PPs and IEs (purple, lambda-like PPs; light blue, other PPs; green, IEs and the LEE element),
the second circle shows the nucleotide sequence positions (in Mbp), the third and fourth circles show CDSs transcribed clockwise and
anticlockwise, respectively (gray, conserved in all eight other sequenced E. coli strains; red, conserved only in the B2 phylogroup;
yellow, variable distribution; blue, E2348/69 specific), the fifth circle shows the tRNA genes (red), the sixth circle shows the rRNA
operons (blue), the seventh circle shows the G+C content, and the eighth circle shows the GC skew. (B) EPEC strain E2348/69
plasmids. The boxes in the outer and inner circles represent CDSs transcribed clockwise and anticlockwise, respectively. Pseudogenes
indicated
by black boxes, and other CDSs are indicated by the colors described above for panel A.
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3. are
genome
analysis
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Structural genomics
NMR
DNA
0101#01001010#10111010#
01010001#10010#1001#101
10010#100100100101011#0
3. genome analysis
Algorithm
Residue



THR
0.0
147.7
172.9
THR
107.2
-125.3
187.4
CYS
123.4
63.6
103.7
PRO
60.3
83.9
-116.7
Protein Structure
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