Theory of
Combinatorics
Codes
on words
Formal
Languages
Molecular
Computing
Formal
Theory of
Languages
Codes
THESIS
On the power of
classes of splicing
systems
Combinatorics
Molecular
on words
Computing
Dottoranda: Rosalba Zizza (XIII ciclo)
Supervisori: Prof. Giancarlo Mauri
Prof.ssa Clelia De Felice (Univ. di Salerno)
Tom Head 1987 (Bull. of Math. Biology)
“ Formal Language Theory and DNA:
an analysis of the generative capacity
of specific recombinant behaviors”
SPLICING
LINEARE
CIRCOLARE
Modelli non
convenzionali di
calcolo
Una motivazione generale per lo splicing
Gearchia di Chomsky
RE
mT
CS
LBA
CF
PDA
REG
DFA
Splicing systems
H(F1 , F2) ; C(F1 , F2 )
F1 , F2 {FIN , RE, CS, CF,REG}
1) Processo generativo del linguaggio
2) Prove di consistenza del sistema splicing
LINEAR SPLICING
restriction
enzyme 2
restriction
enzyme 1
ligase enzyme
Linear splicing systems
(A= finite alphabet, I A* initial language)
Paun’s definition
x u1u2 y,
x u1 , u2 y
Definitions
SPA = (A, I, R)
wu3u4 z
R A* | A* $ A* | A* rules
 A*
wu3 , u4 z
r = u1 | u2 $ u3 | u4  R
x u1 u4 z ,
wu3 u2 y
Splicing language L(SPA) , H(F1, F2)
Some known results [Head; Paun; Pixton; 1996-]
• Fin  H(Fin, Fin)  Reg
• Fin  H(Fin, Reg)  Re
• H(Reg, Fin) = Reg
Comparing the three definitions of (finite) splicing
L(SH )  L(SPA )  L(SPI )
[P. Bonizzoni, C. Ferretti,
G. Mauri, R.Z., Grammar
Systems 2000, IPL ‘01]
Problem (HEAD)
Can we decide whether a regular language
is generated by a finite splicing system?
[P. Bonizzoni, R.Z.,
Tech Rep. 254-00 DSI, submitted]
Theorem
L regular language 0-generated 
L generated by finite splicing
Monoide sintattico:
Rappresentazione di L attraverso classi di congruenza
Proprieta’ delle classi di congruenza...
regole splicing
CIRCULAR SPLICING
restriction
enzyme 2
restriction
enzyme 1
ligase enzyme
Circular languages: definitions and examples
w, w A*, w
• Conjugacy relation on A*
Example
abaa, baaa, aaab,aaba
• A~ = A*  ~ = set of all circular words
• Circular language
C A~
L
L
(A linearization of C, i.e. ~L =C)
{w  A*| ~w C}= Lin(C)
(Full linearization of C)
w=xy, w = yx
are conjugate
~w = [w] , w A*
~
set of equivalence classes

A*
~ w 
A*  ~
~L = {~w | w L} (circularization of L)
C
C
Il nostro “approccio”...
Linguaggi Circolari
Regolari
Linguaggi Formali chiusi sotto coniugazione
Regolari
Circular splicing systems
(A= finite alphabet, I A~ initial language)
Paun’s definition
~hu u ,
1 2
u2 hu1
SCPA = (A, I, R)
 A~
~ku u
3 4
R A* | A* $ A* | A* rules
r = u1 | u2 $ u3 | u4  R
u4ku3
Definition
~ u hu u ku
2
1 4
3
Splicing language C(SCPA)
In the literature...
Other models, additional hypothesis (on R)
Other definitions of circular splicing
(Head, Pixton)
Problem 1
Structure of circular regular languages
(regular languages closed under
conjugacy relation)
Problem 2
Characterize circular regular languages
generated by finite circular splicing
Circular finite splicing languages
and Chomsky hierarchy
CS~
CF~
Reg~
~((aa)*b)
~(aa)*
I= ~aa  ~1, R={aa | 1 $ 1 | aa}
~(an
bn)
I= ~ab  ~1, R={a | b $ b | a}
Contributions
[P. Bonizzoni, C. De Felice, G. Mauri, R.Z., Words99, DNA6 (2000),
submitted]
-Reg~  C(Fin, Fin)
Fingerprint closed
star languages
X*, X regular
group code
Reg~
cyclic
languages
Cir (X*)
X finite
weak cyclic,
altri esempi
~ (a*ba*)*
-Comparing the three def. of circular splicing systems
C(SCH )  C(SCPA )  C(SCPI )
L  A*
star language = L regular, closed under
conjugacy relation, L=X*, with X regular
Why studying star languages?
Proposition
Given SCPA=(A,I,R), if I  ~ X*, ~ X* star language
then the circular language generated by SCPA is 
“Consistence” easily follows!!!
The unique problem is the generation
of all words of the language
~
X*
Proposition
X* star language, X finite set 
~ X* generated (by splicing)
Theorem
X* star language AND fingerprint closed
~X* generated (by splicing)

X regular group code. For any automaton A and
for any cycle c in A, c  X*.
(X* is fingerprint closed)
The case of one-letter alphabet
 Each language on a* is closed under
conjugacy relation
Theorem L  a* is CPA generated
L = L 1  (aG ) +
• L 1 is a finite set
•  n : G is a set of representatives of the elements in a subgroup G’ of Zn
• max{ m | am  L 1 } < n = min{ ag | ag  G } = min aG
Uniform languages characterization
J  N, L = AJ = j  J Aj = {w A * | |w|=j}
Complexity description / minimal splicing system
Theorem
L  a* generated by a finite circular (Paun) system,
then L is generated by ({a}, I, R) with
I = L1  aG
R= { an | 1 $ 1 | an }
Examples
• L = { a 3 , a 4 }  { a 6 , a 14, a 16 }+
I={a 3 , a 4 , a 6 , a 14, a 16 } R={a6
| 1 $ 1 | a6 }
• L = { a 3 , a 4 , a5 , a7 }  {a8 , a9 , a10 , a12 , a13 , a14 , a15 }+
I={a3 , a4, a 5, a7, a8, a9, a10, a12 , a13 , a 14, a15 } R={a8
| 1 $ 1 | a8 }
Given L  a* , we CAN NOT DECIDE whether
L is generated by a circular (Paun) splicing system
(Rice’s theorem)
Problem: Given L  a* , regular ,
can we decide whether L is generated by a
circular (Paun) splicing system?
Probably YES
!!!
Sketch:
L = { a 3 , a 4 }  { a 6 , a 14, a 16 }+
G ={6, 14, 16 }
G’ = {0, 2, 4} subgroup of Z6
• |Fl |=1 , Fl ={qn }
a 12
a 11
• p|n:
{ a 3, a 4, a 6}
n
p
Computational power of Pixton’s systems
Pixton’s definition
~h ,
SCPI = (A, I, R)
~ h
h
Remind
 A~
R A*  A*  A* rules
(, ;  ), (, ;  )  R
h 
~ h  h 
C(SCH )  C(SCPA )  C(SCPI )  ~Reg
Pixton
recombinant
process
~
((A2)* (A3)*)  ~Reg \ C(SCPI )
F
Class of circular regular languages generated by Pixton
• X* generated by regular group codes  F
• All known examples of regular splicing languages  F
•
~
A* \ a+ = ~(a*ba*)* (star free language)
• ~(aa)*b
• ~{w  A* |  h,k  N : |w|a =2h+1, |w|b =2k+1}
• ~(aa)*a,
~(ab)*a  ~(ab)*b
(Linear splicing) Inclusion results
Characterization of regular (finite) splicing languages
(Circular splicing) Fingerprint closed star languages, cyclic languages,
weak cyclic languages, unary languages (CODES)
Pixton systems (subclasses or regular languages)
(Formal languages) Characterization of circular regular languages
(Linear splicing) Problems on descriptional complexity
(Circular splicing) Pixton systems
Unary Languages:
linear splicing vs. circular splicing