Bioinformatic Tools and Molecular Tables — 719
A Collection of Useful Bioinformatic Tools and Molecular Tables
The Genetic Code
2nd Position
U
C
A
G
UUU Phe
UUC Phe
UCU Ser
UCC Ser
UAU Tyr
UAC Tyr
UGU Cys
UGC Cys
U
C
UUA Leu
UUG Leu
UCA Ser
UCG Ser
UAA Stop
UAG Stop
UGA Stop
UGG Trp
A
G
CUU Leu
CUC Leu
CCU Pro
CCC Pro
CAU His
CAC His
CGU Arg
CGC Arg
U
C
CUA Leu
CUG Leu
CCA Pro
CCG Pro
CAA Gin
CAG Gin
CGA Arg
CGG Arg
A
G
AUU Ile
AUC Ile
ACU Thr
ACC Thr
AAU Asn
AAC Asn
AGU Ser
AGC Ser
U
C
AUA Ile
AUG Met
ACA Thr
ACG Thr
AAA Lys
AAG Lys
AGA Arg
AGG Arg
A
G
GUU Val
GUC Val
GCU Ala
GCC Ala
GAU Asp
GAC Asp
GGU Gly
GGC Gly
U
C
GUA Val
GUG Val
GCA Ala
GCG Ala
GAA Glu
GAG Glu
GGA Gly
GGG Gly
A
G
U
C
3rd Position
1st Position
2
Appendix
A
G
The codons are read as triplets in the 5' → 3' direction, i.e., left to right.
Termination codons are in bold.
719
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7 2 0 — Appendix
IUPAC Nucleotide Codes
Code
A
C
G
T
U
Y
R
M
K
S
W
H
B
V
D
N
Members
Nucleotide
A
C
G
T
U
C or T(U)
A or G
A or C
G or T(U)
G or C
A or T(U)
A or C or T(U)
G or T(U) or C
G or C or A
G or A or T(U)
G,A,C or T(U)
Adenine
Cytosine
Guanine
Thymine (DNA)
Uracil (RNA)
pYrimidine
puRine
aMino
Keto
Strong interaction (3 H bonds)
Weak interaction (2 H bonds)
not-G
not-A
not-T
not-C
aNy base
IUPAC Amino Acid Codes
3-Letter Code
1-Letter Code
Ala
Arg
Asn
Asp
Cys
Gln
Glu
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
Asx
Glx
Xaa
A
R
N
D
C
Q
E
G
H
I
L
K
M
F
P
S
T
W
Y
V
B
Z
X
Amino Acid
Alanine
Arginine
Asparagine
Aspartic acid
Cysteine
Glutamine
Glutamic acid
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
Aspartic acid or Asparagine
Glutamic acid or Glutamine
Any amino acid
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Bioinformatic Tools and Molecular Tables — 721
Converting Base Size of a Nucleic Acid → Mass of Nucleic Acid
Number of Bases
Mass of Nucleic Acid
6.6 × 105 Da
3.3 × 105 Da
3.4 × 105 Da
1MDa ds DNA (Na+)
660 Da
330 Da
340 Da
1 kb ds DNA (Na+)
1 kb ss DNA (Na+)
1 kb ss RNA (Na+)
1.52 kb ds DNA
Average MW of a dsDNA
Average MW of a ss DNA
Average NW of an RNA
Converting Base Size
of a Nucleic Acid → Maximum Moles of Protein
DNA
Molecular
Weight (Da)
270 bp
1.35 Kbp
2.7 Kbp
4.05 Kbp
10,000
50,000
100,000
150,000
Amino
Acids
90
450
900
1350
1 µg
1 nmol
100 pmol or 6 × 1013 molecules
20 pmol or 1.2 × 1013 molecules
10 pmol or 6 × 1012 molecules
6.7 pmol or 4 × 1012 molecules
10 µg
50 µg
100 µg
150 µg
Average MW of an amino acid = 110 (Da).
3 bp are required to encode 1 amino acid.
Sizes of Common Nucleic Acids
Nucleic Acid
lambda DNA
pBR322 DNA
28S rRNA
23S rRNA (E. coli)
18S rRNA
16S rRNA (E.coli)
5S rRNA (E. coli)
tRNA (E. coli)
Number of Nucleotides
Molecular Weight
48,502 (dsDNA)
4361 (dsDNA)
4800
2900
1900
1500
120
75
3.2 × 107
2.8 × 106
1.6 × 106
1.0 × 106
6.5 × 105
5.1 × 105
4.1 × 104
2.5 × 104
Mass of Nucleic Acid ↔ Moles of Nucleic Acid
Mass
1 µg/ml of nucleic acid
1 µg of a 1 kb DNA fragment
0.66 µg of a 1 kb DNA fragment
Moles
3.0 µM phosphate
1.5 pmol; 3.0 pmol ends
1 pmol
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7 2 2 — Appendix
Sizes of Various Genomes
Organism
Approximate Size (million bases)
Human
M. Musculus (mouse)
Drosophila (fruit fly)
Arabidopsis (plant)
C. elegans (round worm)
S. cerevisiae (yeast)
E. coli (bacteria)
H. influenzae (bacteria)
3000.0
3000.0
135.6
100.0
97.0
12.1
4.7
1.8
Genomic Equivalents of Species
Organism
Source
of DNA
Human
Mouse
Rat
Bovine
Annelid
Drosophila
Yeast
diploid
diploid
diploid
haploid
haploid
diploid
haploid
pg/haploid a
Genome
3.50
3.00
3.00
3.24
1.45
0.17
0.016
Avg.b
3.16
3.21
3.68
3.24
1.45
0.18
0.0245
µg quantity
for Genome
Equivalence
10.0
8.57
8.57
9.26
4.14
0.486
0.0457
Number
of Genomes
× 106
2.86
2.86
2.86
2.86
2.86
2.86
2.86
a pg/haploid genome was calculated as a function of the tissue source. Genomic equivalence
was calculated given that 10 µg of human genomic DNA contains 2.86 × 106 genome copies.
b Average of all values given in each tissue for that species.
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