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ISSUE 2, VOLUME 6 (December 2012)

ISSN: 2250-1797

Bipartite Semigraph Structure in DNA Splicing System

S.JeyaBharathi1, M. Angayarkanni2 S.Sinthanai Selvi3 R.Anusha4
Department of Mathematics
Thiagarajar College of Engineering1
Mannar Thirumalai Naicker College3
Research Scholar - Thiagarajar College of Engineering2, 4
Madurai, Tamilnadu, India.
_____________________________________________________________________________
Abstract Splicing plays a vital role in DNA Computing. We associate the graph splicing
scheme of Rudolf Freund [3] with semigraphs introduced by E. Sampath Kumar [10]. In this
paper we discussed the properties of the odd and even cut bipartite semigraph structures of
double stranded DNA molecules and characterized the number of independent sets and
languages produced by them. This system stands as a theoretical model for the categorization of
n-cut splicing system.
Keywords- Bipartite semigraph, n- Cut Splicing.
_____________________________________________________________________________
I.INTRODUCTION
Tom Head introduced the new concept of splicing system for describing the recombinant
behaviors of double stranded DNA molecules. Since then the theory of splicing systems has
become a new interesting area of formal Languages Theory. DNA exists not only as Linear
Molecules but also as Circular molecules. Investigating the Complex structures of genes, Rudolf
Freund [3] suggested graphs as more suitable objects for modeling and exhibit the relation
between regular graph splicing systems on graphs and splicing systems on strings. DNA
sequences are three-dimensional objects in a three dimensional space. Hence graphs seem to be
more suitable objects for describing complex three-dimensional objects independently from their
actual position in three dimensional spaces. It had been observed that, at the time of splicing
DNA molecule holds the characterisation of semigraph. This semigraph is more powerful than
graph model. This presents communication volume accurately. Semi graph model will eventually
replace graph partitioning in scientific computing. The theory of splicing systems on bipartite
string languages gave different perceptiveness in specifying non-context free features.

II PRELIMINARIES
2.1. Splicing System:
Splicing is a model of the recombinant behaviour of double stranded molecules of DNA under
the action of restriction enzymes and ligases. A single stranded of DNA is an oriented sequence of
nucleotides A, C, G & T but since A can bind to T & G to C, two strands of DNA bind together to
form a double stranded DNA molecule, if they have matching pairs of nucleotides when reading
the second one along the reverse orientation.

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2.2. Graph:
A graph over V is a triple (N, E, L) where N is the set of nodes, E is the set of edges of the
form (n, m) with n, m N, n m and L is the function from N to V assigning a label from V to
each node of N. The set of all graphs over V is denoted by (V).
2.3. Graph splicing scheme:
A graph splicing scheme is a pair (V, P), where V is an alphabet & P is a finite set of graph
splicing rules of the form ((h [1], E' [1]) (h [k], E' [k]); E), where k 1& for all i with 1
i k,
h[i] (V), h[i] = (N [i], E [i], L[i]),
E[i] E [i],
The node sets N[i] are mutually disjoint, and E must obey the following rules:
1. Each edge (n, m) E' [i] divided is supposed to be into two parts, i.e., the start part (n, m] and
the end part [n, m).
2. The elements of E are of the form ((n, m], [n', m')),
where (n, m) and (n', m') are edges from U1 i k E' [i].
3. Every element from {(n, m], [n, m) / (n, m) U1 i k E' [i]} must appear exactly once in a
pair of E.
2.4. Graph splicing rule:
Let P = ((h[1], E'[1 ),, (h[k], E'[k]); E) be a graph splicing rule, and let c(V). If we
can select k different graphs g[1], , g[k] from , then we can apply p to , which yields
some sc(V) in the following way:
For all i with 1 i k, h [i] is a subgraph of g[i], where f[i] establishes the injective node
embedding of h[i] into g[i].
The union of g[1], g[k] can be looked at as a single graph g in (V) and the union of the
functions f[i] as a single function f embedding the h[i] into g. From g we now eliminate all
edges from U1 i k f( E'[i]), but add all edges (f(n), f(m')) such that ((n, m], [n', m')) E, which
yields the uniquely determined union of k' weakly connected graphs g' [1], , g' [k']) .
Example 2.1:

The graph G represents 1-Cut splicing ( u C1 ) with the Semivertices V= {1', 2', 3', 4', 5', 6'} and the
Semiedges E={(1, 1'), (2, 2'), (2. 3'), (5, 5'), (5, 4'), (4, 6')}. Here |V ' | = 6 and |E' | = 6.

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1-Cut spliced semigraph

G1

III. BIPARTITE SEMIGRAPHS

3.1 Semi Graph:
A semigraph G is a pair (V, X) where V is a non - empty set whose elements are called vertices
of G and X is a set of n - tuples called edges of G of distinct vertices for various n 2, satisfying
the following conditions:
S.G-1 Any two edges have at most one vertex in common.
S.G-2 Two edges (u1, u2, u3, ..., un) and (v1, v2, v3, , vm) are considered to be equal if and only
if (i) m = n
and (ii) either ui = vi or ui = vn-i+1 for 1 i n. Thus the edges (u1, u2, u3, .., un) are the
same as the edge
(un, un-1, .., u1).
3.2. Semivertices:
Let G be a graph, when splicing G, we obtain new vertices which are called as semi vertices
denoted by V', where |V' |=p'.
3.3. Semiedges:
Let G be a graph when splicing G, we obtain new edges by decomposition of edges which are
called as semi edges denoted by E', where |E' | = q'.
3.4.. Independent set:
A set S of vertices in a spliced semigraph G = (V, X) is independent set if no two vertices are
adjacent.
3.5. Bipartite Semigraphs [10]:
G is bipartite if its vertex set V can be partitioned into sets {V1, V2} such that both V1 and V2
are independent.
3.6. uC n .- Represents a n-cut spliced semigraph where u is the string, c- The number of cut and nThe number of splicing.
Theorem 3.1:
Every spliced semigraph forms two bipartite semigraphs.
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Proof: Let us assume the nCut spliced semigraph uC n of L = n + 2. After applying n Cut
splicing we have two sets of spliced semigraphs which are nothing but a tree since each spliced
semigraph contains no cycles and it is connected , q + q' = P - 1. Let there be m number of
vertices after n-Cut splicing. We have {v1, v2 vl, vl+1 vm}. Here l = m. Since after n-Cut
splicing (uC n ), the two spliced semigraphs have equal number of vertices. Consider the edge e =
(vivj), ij and i, j=1,2, , l. Place vi, i=1,2, , l in the vertices set V1 and the adjacent vertices vj
in the another vertices set V2. Let the vertices say vk be adjacent to vi and vr adjacent to vj are kept
in the corresponding opposite vertices set respectively.Consider the semiedge e' = (vgvh'), g, h
=1,2, , l. and proceed as edge. Continuing the above process we get the bipartite
graph.Similarly consider the edge e = (vivj), ij and i, j=l+1, l+2, , m. Place vi, i=1, 2,, l in
the vertices set V1 and the adjacent vertices vj in the another vertices set V2. Let the vertices say
va is adjacent to vi and vb adjacent to vj are kept in the corresponding opposite vertices set
respectively. Consider the semiedge e' = (vgvh'), g, h = l+1, 2, , m and proceed as edge.
Continuing the above process we get another bipartite graph. we get two bipartite semigraph
which are disconnected. Hence every spliced semigraph forms two bipartite semigraphs.
Example 3.1
Representation of 1-Cut (uC 1 )spliced bipartite semigraphs is as follows:

G2

G3

Example 3.2
Representation of 2-Cut (uC 2 )spliced bipartite semigraphs are as follows:

G4

G5

Theorem: 3.2
Every n-Cut spliced semigraph forms a bipartite graph with partite sets {V1, V2} such that V = V
1U V2 then
|V| =

n(V1) = n(V2), if n is even

n(V1 ) n(V2) , if n is odd
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Proof. Let V1 and V2 represent the independent sets of any n-cut bipartite semigraph graph. The
number of vertices belongs to the independent sets V1 and V2 varies according to the value of n,
by instance, for odd-cut splicing the number of vertices in V1 and V2 are r+2 and r respectively.
But in terms of even n, n(V1) = n(V2) by observing. Thus the cardinality of the independent
sets of uC n remains same for every n is even.
Theorem: 3.3
Every n-cut spliced semigraph has maximum independent set S with |S|=

n+2, if n is even

n+3, if n is odd
be the n-cut spliced semigraph. Every uC n has bipartite graph with partite sets

Proof: Let uC n
V1 and V2 with
|V1| = n+2, if n is even and |V2| =

n+2, if n is even

n+1, if n is odd
independent

n+3, if n is odd Therefore there exist a maximum

n+2, if n is even

set uC n with |S|=

n+3, if n is odd
IV. LANGUAGES ON N-CUT SPLICING SYSTEM WHEN THE VERTICES TAKES THE
VALUES as and bs.
Theorem: 4.1
L(S) =

a n+1 b n+3,
n+2

n 1 is odd

n+2

a
b
,
n 2 is even where S is the maximum independent set of n-cut
bipartite semigraph having partite sets V1 and V2 such that S = V1 V2
Proof: Let G1 be the bipartite graph formed from the n- cut spliced semigraph. Let V1 and V2 be
the two partite sets of G1. Let V1 and V2 consists of the set of vertices takes the values as and bs
respectively .From theorem (3.2) and (3.3),
L(S) =

a n+1 b n+3,

n 1 is odd

a n+2 b n+2 , n 2 is even

Example: 4.1
Let G6 and G7 be the 1 and 2-cut spliced bipartite semigraphs. The language produced by the
independent sets are given by L(S) = { a2b4} and L(S)={a4b4} respectively.
1-cut spliced bipartite semigraph
V1
b
b

2-cut spliced bipartite semigraph

V2

V1

V2
a

a
b

a
b

b
a

G6

G7

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Result: 4.1
Replacing b=a in V1 and V2, The language produced by the independent set
L(S) = {a2n+4
n 1}.

S is given by

Result: 4.2
Replacing b=a in an alternating sequences in V1 and V2, L(S) = {a n+2 bn+2,

n 1}.

Example: 4.2
Replacing a=b in an alternating sequence in V1 and V2, the language produced by the
independent sets are given by L(S) = {a3b3}, L(S) = {a4b4} for G8 and G9 respectively.

b
b
a

a
b

b
G8

G9

Result: 4.3
There exists equal number of pendent vertices in the partite sets of the n-cut spliced bipartite
semigraph
for every n is even.
Theorem: 4.2
The eccentricity of an n-cut Spliced bipartite semigraph is of length n+2 units for all n1.
Proof: The eccentricity of the n- cut spliced semigraph E (uCn) is the maximum distance from the
initial vertex to the final vertex. The number of pendent vertices in each cut is derived from the
semiedges of the spliced semigraph. Each semiedge is of edge length e/2, for an n-cut spliced
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semigraph there exist r/2 set of pendent vertices which belongs to the semiedges out of r
vertices. Travelling from the initial vertex vi the path that covers the maximum number of
complete edges reaches the final vertex vj which belongs to the semiedge Es. Thus the number of
edges in the maximum edge cover is equal to p (e/2) + q (e) = n+2.
V. NOMENCLATURE
uC n .- Represents the nth-cut spliced semigraph where u is the string, c- the number of cut and
n- the number
of splicing.
SSG - Spliced Semigraph
n (V) - number of vertices
n (X) -number of edges
L(S)- Language produced by the maximal independent set.
VI. ACKNOWLEDGEMENT
The authors gratefully acknowledge the support from the Grant by UGC coming under
Major Research Project- [41-800/2012].
VII. REFERENCES
[1] L.Adleman, Molecular computation of solutions to combinatorial problems, Science,
266(1994), 1021-24.
[2] J.Dassow, V.Mitrana, Self Cross-over Systems, Discrete Mathematics and Theoretical
Computer Science, Springer Series, G.Paun (Ed.), 1998, 283-294.
[3] R.Freund, Splicing Systems on Graphs, Proc. Intelligence in Neural and Biological
Systems, IEEE
Press, 1995, 189-194.
[4] K. Gnanamalar David , K.G.Subramanian and D.Gnanaraj Thomas, A Note on Graph
Splicing Languages, Lecture Notes in Computer Science, Vol.2340, Springer-Verlag, 381390, 2001.
[5] F.Harary, Graph Theory, Addison-Wesley, Reading, Mass, (1969).
[6] T.Head, Formal Language Theory and DNA An analysis of the generative capacity of
recombinant behaviors. Bulletin of Mathematical Biology, 49,1987, 735-759.
[7] N.Jonoska, 3D DNA Patterns and Computation, Proc. Molecular Computing, India, 1998,
20-32
[8] S.Jeya Bharathi, J.Padmashree, S.Sinthanaiselvi, Semigraph structure on DNA splicing
system, Sixth international conference on Bioinspird computing:Theories and
applications, IEEE-computer society, Penang, Malaysia ,2011,182-187.
[9] A.Salomaa, Formal Languages, Acade mic Press, New York, 1973.
[10]

E.Sampathkumar, Semigraphs and their Applications, Report on the DST project, 2000.

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