Laboratory for Mathematic Methods and Models in Bioinformatics, IITP RAS
Model of RNA-related regulation in bacteria
Examples
Escherichia coli - trp
Escherichia coli mutant @75 - trp
Escherichia coli mutant @132 - trp
Escherichia coli K12 - his
Rhodopseudomonas palustris - trp
Vibrio cholerae - trp
Corynebacterium diphtheriae - trp
Sinorhizobium meliloti - trp
Streptomyces avermitilis - trp
Streptomyces coelicolor - trp
Rhizobium leguminosarum - trp
Sequence
Amino acid(s)
ala / alanine
arg / arginine
asn / asparagine
asp / aspartic acid
cys / cysteine
gln / glutamin
glu / glutamic acid
gly / glycine
his / histidine
ile / isoleucine
leu / leucin
lys / lysine
met / methionine
phe / phenylalanine
pro / proline
ser / serine
thr / threonine
trp / tryptophan
tyr / tyrosine
val / valine
Concentration
Exclude positions (pos1,len1,pos2,len2...) ==>
Model description
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Energy calculation
α
B
loop
B
bulge
B
intloop
C
l
max
T°
Transitions
Formula
Symm
Asymm
Asymm+q
Symm+q
MAX #
κ
λ
pol
λ
rib
λ
ura
Q
S
pol
S
rib
Polymerase slowdown
β
L
1
p
0
r
0
δ
Hairpin
MAX
SUM
MAXbulge
MAXintloop
Limits
Helix
Hypohelix
MINloop
MAXloop
L
pol
L
rib
U
minlen
U
fraction
U
last #
Repetition
Seed
Lic.
Output
std
more
most