RNA-type matchings

16 2014 .
1 Colored matching
A word in the alphabet A is a nite sequence of symbols a
i
A. For instance,
if A = {0, 1}, we have nite binary sequences as words. In particular, w =
101101 is a word, and we denote |w| = 6 (the length of the word). We will
also say that w has 6 positions numerated 1, 2, . . . , 6. The symbol at position
i is referred to as w
i
. In our case, say, w
2
= 0.
A matching on w is a set of pairs of positions in w such that all these
positions are dierent. Say, M = {(1, 4), (3, 5)} is a matching. The order of
positions in the matching does not make any dierence, that is, {(1, 4), (5, 3)}
is the same matching M. For convenience, we will use the ascending order,
that is, we will always write (3, 5), not (5, 3).
Let us interpret positions of the word as the set of points (i, 0), i =
1, 2, . . . , |w|, in the plane R
2
. They are positive integers on the x-axis. A
matching can be visualized as a set of arcs that connect the corresponding
pairs of positions. We assume that these arcs are semicircles above the x-
axis. In our case (matching M) two arcs have an intersection point. We say
that the matching is crossless if its arcs are all disjoint, that is, if they have
no intersections with each other.
Let us say that the pair (i, j) of positions in w is admissible if w
i
=
w
j
. The matching M will be called admissible if it is crossless and all its
pairs are admissible. For instance, the matching M
a
= {(1, 6), (2, 5), (3, 4)}
is admissible and M
b
= {(1, 3), (2, 5)} is not (there is a crossing).
We are looking for a maximal admissible matching on a given word w,
that is, for a matching that contains a maximal number of pairs. In our
example, M
a
is the unique maximal matching, and it is also complete, that
is all the positions of w are used.
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Denote by |M| the number of positions that are matched by |M|. For
instance, |M
b
| = 4. Denote also d(M) = |w| |M| (the defect number of M).
By d(w) we denote the minimal value of d(M) over all admissible matchings
M of the word w.
Question 1.1. Let w be a binary word of length |w| and let M be a maximal
admissible matching for w. Which values of |M| are possible?
2 RNA-type matchings
We may change the denition of admissible pair of positions as follows: (i, j)
is admissible if w
i
= w
j
. Then we ask the same question:
Question 2.1. Let w be a binary word of length |w| and let M be a maximal
admissible matching for w. Which values of |M| are possible?
The rst model that was initiated by the research of the secondary struc-
ture of RNA chains is the following one. Let A = {1, 2, 3, 4} and let admissible
pairs of colors be (1, 2) and (3, 4).
Question 2.2. Suppose the word w in alphabet A is generated at random
(Bernoulli scheme, where each symbol of A has equal probability at each
position of w independently of the rest of the word). What is the probability
that the pair (i, j) is admissible? The same question for the four-color case
in the colored matching"scheme.
3 General matching pattern
Here we do not consider words any longer! Let us choose an integer interval
1, . . . , N. Some pairs (i, j) of positions within this interval will be declared
admissible (or matchable). This can be done in dierent ways.
For instance, given a parameter p [0, 1], we may declare each pair (i, j)
matchable with probability p (and unmatchable otherwise). In words, we are
tossing a biased coin for each pair (i, j), independently. If we draw an edge
between i and j for each matchable pair (i, j), we get an Erdos-Renyi random
graph.
The problem is, again, to count |M| for a maximal crossless matching M.
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4 String matching
Let us begin with the following problem. We have a string with a nite
number of beads"on it. The beads have no size, just points on a line, but
they may be of dierent color"(there is a nite set of colors). Then we lay
the string on a plane in such a way that some pairs of beads of the same
color contact with each other (the points coincide) but the string has no
self-intersections. What is the maximal number of such pairs?
Another problem is an extension of the colored matching and other cross-
less matchings. The dierence is that now we allow the matching arcs to
be drawn either above or below the x-axis. We will use the name string
matchings"for admissible matchings in this sense.
Question 4.1. Is it the same as the beads-on-a-string"model? What if the
string is closed (like a circle)?
Question 4.2. Suppose A = {1, 2, 3} and there is an even number of each
color in the word w. Does it always exist a complete string"matching in this
case?
5 Asymptotic properties of string matching
Clearly, the two-sided version of the matching problem has larger matchings
than the one-sided version. The question is if now the relative defect of a
long word in the alphabet {1, 2, 3} vanishes as |w| .
I am not aware of an algorithm that could count the minimal defect in a
reasonable time.
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