Index

A

aa2nt, 183, 222
aacount, 184, 222
abs, 7, 218
accession number, 175, 177
acos, 7, 218
acot, 7, 218
Aligned Sequences, window, 196, 206
alignment global, 191
local, 193
multiple, 194, 208
Needleman-Wunsch, 193
pairwise, 190, 196
Smith-Waterman, 193
alphabet amino, 172, 183
DNA (or dna), 172, 183
RNA (or rna), 3, 16
aminolookup, 9, 188, 222
and, 35, 219
Andrade-type expression, 90
ans, 8, 218
answers, to selected exercises, 93, 48, 129, 167, 211
Archimedes’ spiral, 89
arithmetical operations, 6
with arrays, matrices, 19, 28
operators, 28
array
division, 23
exponentiation, 23
element-wise (or array, or element- by-element) operation, 26
multiplication, 23
Arrhenius equation, 14, 87
arrow key, 6
assignment, 6, 217
asin, 7, 218
aster, prairie, height, 91
astroid, 89
assignment operator, 6
atan, 7, 218
axis, 57, 220

B

bacteria
Escherichia coli (E. coli), 163, 210
population, 41, 164
cells, 47
culture, 166
bar, 78, 220
bar3, 78, 220
basal metabolic rate (BMR), calculator, 117
basecount, 188, 222
baselookup, 188, 222
batch
enzyme, 17
reactor, 164
bio-fuel (ethanol), 165
Bioinformatics toolbox, 172
bio-oil, viscosity, 90
bioreactor, continuous stirred-tank (CSTB), 170
blastncbi, 181, 222
blood, mass flow rate, 45
body mass
index (BMI), 116
calculator, 116
box, box on/off, 68, 220
brackets, 15, 17, 218
Brusselator-type, partial differential equation, 166

C

cancer
incidence data fitting, 124
carcinogen, 124
chemostat, 143
clabel, 78, 220
clc, 6, 218
clear, 10, 218
codoncount, 189, 222
colon (:), 6, 217
color, property name, 61
colormap, 68, 220
Command Window, 6
comment (%), 6, 11, 217
compound, amount, 121
concentration
compound, 40
change
two species, 79
with time and temperature, 87
with time and coordinate, 157, 170
in opposed reaction, 79
molar, solute in water, 91
solution (dilution), 43
units, conversion, 118
conditional statements if … end, 37, 219
if … else … end, 37, 219
if … elseif … else … end, 37, 219
while … end, 38, 219
contour, 78, 220
contour3, 78, 220
cos, 7, 218
cross-cap, 90
Current Folder, window, 3, 5
curve
fitting, 113
two or more on single plot, 53
cylinder, 77, 220

D

data (bioinformatical)
format, 173
reading files, 175
search engine
BLAST, 174
FASTA, 174
storing files, 174
databases
public, 173
accession, number, 175
management, commands, 179
NCBI, 173
NCBI GEO, 173
GenBank, 173
GenPept, 173
GO, 173
EMBL, 173
PDB, 173
PFAM, 173
decay, radioactive substances, 46, 129
density
air, 83
mosquito, 47
nucleotide, 186
solution (dissolving), 118
derivative, 110
Desktop, windows, 3
det, 27, 219
determinant, 27
diag, 26, 219
diff, 110, 221
differential equations
ordinary, 133
partial, 151
diffusion, transient, 1D, 86, 152, 166
dilution, 43, 100
dimercount, 189, 222
disp, 11, 220
display formats, 8
dissociation, 14, 123
distance
between two molecules, 13
score, 190, 195
division, left, right, 6, 22, 26, 217
DNA
alphabet, 172
Hominidae mitochondrial, 208
volume, 12, 97
sequence, 172
bases, table, 29
doc, 9, 218
drug, dissolution rates, 164

E

Editor Window, 3, 96
element-wise (or element-by-element) operations, 23
ellipsoid, 90
else, 37, 219
elseif, 37, 219
emblread, 181, 222
end, 17, 37, 219
equal to, relational, 34, 217
equation, non-linear algebraic, 14, 106
equations, set of linear, 21, 40, 48, 106
exp, 7, 218
extrapolation, 104
eye, 22, 26, 219

F

factorial, 7, 218
Fahrenheit/Centigrade, degrees, 127
false, 35
false, value, 34
Figure window, 50
file
saving/running, 102–3
find, 35, 219
fitting, polynomial, 23, 113
floor, 7, 218
flow control, 33, 219
fluid, cooling, Newton’s law, 14
for, 37, 219
format, 220
short, 8
long, 8
format
FASTA, 174
PDB, 174
SCF, 174
formatting
text string, 60
2D plots, 57, 62
3D plots, 67
Fourier series, the first terms, 46
fplot, 77, 220
fprintf, 11, 220
function
arguments, input/output, 100
definition line, 101
elementary, 5, 218
file, saving/running, 102, 103
Gaussian, elliptic, 85
help lines with comments, 102
user-defined, 100
function, command, 100, 218
fzero, 107, 221

G

gastrointestinal (GI), tract, 164
genbankread, 178, 222
genpeptread, 180, 222
getblast, 182, 222
getembl, 179, 222
getgenbank, 179, 222
getgenpept, 179, 222
getgeodata, 180, 222
getpdb, 180, 222
global, 102, 218
Greek characters, 60
grid, 57, 220
growth
bacteria, 47, 82, 110, 129
microorganism, curve, 82
gtext, 59, 220

H

help, 7, 218
help, browser/window, 8
help graph2d, 76, 218
help graph3d, 76, 218
help specgraph, 76, 218
hemoglobin, muscle, 45
hexosaminidase
Domestic mouse, 175, 194
human, 204, 211
Norway rat, 175, 204
hist, 73, 220
histogram, 75, 91
hold on/off, 53, 228
human
mutant, 180
hormone, 180
protein, 181

I

i, imaginary part of complex number, 10, 218
identity matrix, 22
if, 37, 219
indefinite loop, 38
inf, 10, 218
influenza, 1918 pandemic data, 163
input, 99, 220
input, parameters/arguments of function, 100
integer, random number, 27
integration, 108
integration, numerical method
Riemann, 128
Simpson, 108
trapezoid, 109
interp1, 105, 221
interpolation, method, 105
cubic, 105
spline, 105
linear, 105
inv, 22, 219
inverse
matrix, 22
trigonometric functions, 7, 218

J

j, imaginary part of complex number, 10, 218

K

Kinematic viscosity, bio-oil, 90
kinetics, Michaelis–Menten, 141, 167

L

Langmuir’s isotherm, 92
left division, 6, 22, 217
legend, 59, 220
lemniscate, 89
length, 26, 219
less that, relational, 34, 217
linewidth, 51
linspace, 16, 219
log, 7, 218
log10, 7, 218
logical
functions, 35
operators (commands), 35, 219
variables, 35
loglog, 77, 220
lookfor, 9, 218
loop, 37
Lotka-Volterra, model, 145

M

marker, type specifiers, 51
markeredgecolor, 51
markerfacecolor, 51
markersize, 51
matrix
addition/substraction, 19
multiplication, 20
division, 22
determinant, 27
identity, 22
inverse, 22
size, 10, 26
max, 27, 219
mean, 27, 219
mesh, 66, 220
meshgrid, 65, 220
m-file, 5, 95, 104
min, 27, 219
mitochondrial, DNA sequence
Eastern Lowland gorilla, 208
Jari orangutan, 208
Russian Neanderthal, 208
Chimp, Troglodytes, 208
Western gorilla, genome DNA, 198
modifiers, for text, 60
molviewer, 181, 222
molweight, 189, 222
more than, relational, 34, 217
multialign, 194, 222
multialignviewer, 197, 222
Multiple Sequence Alignment Viewer, window, 198
muscle hemoglobin, volume, 45

N

NaN, 10, 218
not, logical, 35, 219
not equal, relational, 34
nt2aa, 206, 223
ntdensity, 186, 222
nucleotide
sequence transformation, 184
density, 186
numbers, display formats, 8, 222
Nusselt number, turbulent flow, 91
nwalign, 192, 222

O

ode113, 135, 221
ode15s, 135, 221
ode23, 135, 221
ode23s, 135, 221
ode23t, 135, 221
ode23tb, 135, 221
ode23i, 135, 221
ode113, 135, 221
ode45, 135, 221
ODE solvers, form, 136
extended form, 140
solution steps, 136
odeset, 170, 222
ones, 25, 219
or, logical, 35, 219
output
commands, 11
parameters/arguments of function, 100

P

parentheses, 6, 15, 18, 217
partial pressure, gaseous component, 91
particle, trajectory, 92
pdbread, 181, 222
pdepe, 153, 222
PDE solver
condition in standard form
boundary/initial, 151, 152
form, 153
steps of solution, 151
percent, symbol, 6, 11, 217
pi, number, 7, 218
pie, 79, 221
charts, 184, 188, 189
pie3, 79, 221
plot
axis, 57
label, in plot editor, 62
limits, 58
bar
two dimensional, 78
three dimensional, 78
color specifiers, 51, 61
contour, command
2D, 78
3D, 78
dot, 6 – 194
editor, 62
formatting, 57, 67, 220
generation
XY (2D), 49
XYZ (3D), 62
grid, 3D, 65
histogram, 73
labels, 58
legend, 59
line
specifiers, 51
3D, 62
logarithmic axis, 77
marker specifiers, 51
mesh
and contour, 3D, 63, 78
command, 3D, 66
multiple
curves (two or more) in a 2D plot, 53
plots on a page, 55
polar, 77
properties, 51
rotation, 67
semi-logarithmic axis, 75
specialised, 73
specifiers, 52
surface reconstruction, 3D, 31
text, 59
two-dimensional, 2D, 49, 220
three-dimensional, 3D, 62, 220
title, 58
viewing angles, 70
plot, 53, 221
plot3, 63, 221
plot editor, Edit Plot button, 62
plotting a table, 50
pola, 77, 221
polyfit, 114, 221
polyval, 114, 221
population
animal, 165
Europe, statistics, 119
bacteria, 41, 128, 129, 164
microorganism, chemostat, 144
Malthus-Verhulst, model, 148
mosquito, 47
NewYork city, 128
prairie aster, height, 91
Prandtl, number, 91
predator–prey, model, 145
prompt (>>), in Command Window, 5
property, in plot command
name, 51
value, 51

Q

quad, 108, 221

R

rand, 25, 219
randi, 25, 27, 219
randn, 25, 219
random numbers, 25
randseq, 183, 222
rate
acceleration, 112
basal metabolic, 117
decay, 121, 129
dissolution, 164
proliferation, 128
dissociation, 123
reactant
breakdown, 120
amount, 137
reaction
consecutive, 120
constant, 107, 123
first order, 87
opposed, concentration, 79
rate, 14, 80, 91, 108, 111, 120, 123, 140, 164
second order, 138
reaction-diffusion, two-equation system, 155
relational operators/commands, 34, 219
reshape, 26, 219
Reynolds, number, 91
Riemann sum
left, 128
right, 129
right division, 6, 26, 217
RNA, alphabet, 183
roughness, height, bio-films, 92
round, 7, 218

S

score
match/mismatch, 191
sequence distance, 195
scoring
heat map, 193
winning path, 193
script file
creating, 95
input values, 99
run, 98
saving, 97
search folder, 98
self-checking, questions, 44, 88, 127, 162, 209
seqdotplot, 194, 222
seqshoworfs, 184, 222
sequence
amino acid, 181–184, 192, 193, 195, 196, 198
analysis, 182
bull (Bos taurus), 211
Chimp Troglodyte, mitochondrial, 208
Eastern Lowland Gorilla, mitochondrial, 208
Escherichia coli, 210
examples, 197
Guinea pig, oxyhemoglobin, 210
human, 180, 204, 206
Jari Orangutan, mitochondrial, 208
mouse (Mus musculus)
hexoaminidase, 195
insulin, 210
nucleotide, 186, 188, 191, 192, 194, 199, 205, 206, 209
Olive Baboon (Papio anubis), 183, 184, 210
Russian Neanderthal, mitochondrial, 208
rat (Rattus norvegicus) hexoaminidase, 194
protein, 206
Rhesus Macaque (Macaca mulatta), 187, 211
ring-tailed Lemur (Lemur catta), 210
score, 190
statistics, commands, 184
utilities, 182
Western Gorilla (Gorilla gorilla), mitochondrion, 198
wild boar, 189
yeast, 210
semicolon, 6, 217
semi-logarithmic axis, 75
semilogx, 75, 211
semilogy, 75, 211
showscore, property, 191, 193
showalignment, 196, 222
Simpson method, 108
size, 26, 219
solver
ODE, 133, 135
PDE, 133, 151
sort, 27, 219
specialized plots, 2D and 3D, 73
sphere, 77, 221
sqrt, 27, 220
statisics, blossom, 30
std, 27, 219
stem, 79, 221
sterilization, spores’ death time, 127
stopping (interruption) indefinite loop, 38
string, input, 28, 99
structure
MATLAB® construction, 173
3D, molecule, 181
strvcat, 26, 220
subplot, 55, 221
subscript, in text string, 60
sum, 27, 220
superscript, in text string, 60
surf, 66, 221
surface, coverage, 92
surfc, 78, 221
swalign, 209, 222

T

table, display, 29
tan, 7, 218
text, 59, 221
text modifiers, 60
three point (…), icon, 98
title, 59, 221
ToFile, property, 175, 178, 179, 180, 181
toolboxes, about, 171
transpose, (’) operator, 19, 220
trapezoid method, integration, 109
trapz, 109, 221
true, value, 34
tumor
angiogenesis, 159
growth rate, 163

V

van der Waals, equation of state, 127
variable
definition, 10
global/local, 102
name, 10
predefined, 10
management, 10
vector
creating, 15
element dividing, 23
and matrix operators, 15
velocity, molecular, gaseous helium, 92
virus, foot/mouse, 179
viscosity, 90, 128
ver, 171, 218
view, 70, 221

W

waist-to-heap, ratio (WHR), 128
web, 175, 222
Web Browser, window, 176
weight
data, histogram, 75
versus height, 32, 91
molar, sequence, 174
molecular, amino acids, 189
screening, 37
who, 10, 218
whos, 10, 218
wind, chill index, 31, 47

X

xlabel, 59, 221

Y

ylabel, 59, 221

Z

zeros, 25, 220
zlabel, 63, 221
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