# 2.3 Modeling the genefinding problem  (Page 2/3)

 Page 2 / 3

## An example: finding cpg islands

This example is taken from the excellent textbook Biological Sequence Analysis: probabilistic models of proteins and nucleic acids by Durbin, Eddy, Krogh and Mitchison. CpG islands are regions of the genome with a higher than normal percentage of C and G bases adjacent to each other. The usual percentage of adjacent CG bases in the genome is about 1%, but in CpG islands that percentage is over 6%. The reason that C followed by G is relatively rare in The "p" in "CpG" refers to the phosphodiester bond between the cytosine and the guanine, and serves to distinguish it from the C and G pairing on the double stranded DNA helix. CpG islands are bioogically intersting because they are in or near 40% of the promoters in mammalian genes and 70% in human promoter genes. CpG islands vary in length between 300 and 3000 basepairs. Thus fixed-length consensus sequence based approaches do not work well for detecting them. Effective identification of of CpG islands can aid in localizing genes in eukaryotes. CpG island detection also serves as an excellent problem to illustrate the power of Markov models.

We will consider two problems.

• Given a short DNA sequence, does it come from a CpG island or not?
• Given a long DNA sequence, find all the CpG islands on it, if any.

## Generative models of biological sequences

We will construct generative models of CpG islands. A generative model produces strings, and the model parameters are tuned to reflect the characteristics of CpG islands.

The simplest probabilistic generative DNA sequence model associates a probability with the occurrence of each base: P(A), P(C), P(G) and P(T) such that these probabilities all sum to 1. For H. influenzae, these probabilities are P(A) = 0.3, P(C) = 0.2, P(G) = 0.2, and P(T) = 0.3. To generate a sequence based on this model, we first choose the length L of the sequence that we wish to construct. Then we draw bases for each position based on the discrete distribution above, as shown in the code fragement below.

```i = 1; while i less-than-or-equal-to L doS[i] = a base drawn from the discrete probability distribution [0.3,0.2,0.2,0.3](for A,C,G,T) i = i+1end```

This model does not capture interdependencies between bases. It assumes that the choice of base in each position of the generated sequence is independent of the bases surrounding it. A more complex model of DNA sequences can be constructed using the theory of Markov chains. In Markov chains, the probability of observing a base at a given position in a sequence is conditioned on the bases preceding it. Thus, Markov chains can model local correlations among the nucleotides. A Markov chain of order 1 assumes that the probability of a base at position i is dependent only on the base at position i - 1. A first order Markov chain can be specified by a probability matrix as shown below.

A first order markov model for generating dna sequences
A C G T
A 0.6 0.2 0.1 0.1
C 0.1 0.1 0.8 0.0
G 0.2 0.2 0.3 0.3
T 0.1 0.8 0.0 0.1

Is there any normative that regulates the use of silver nanoparticles?
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
why we need to study biomolecules, molecular biology in nanotechnology?
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
why?
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
anyone know any internet site where one can find nanotechnology papers?
research.net
kanaga
sciencedirect big data base
Ernesto
Introduction about quantum dots in nanotechnology
what does nano mean?
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
absolutely yes
Daniel
how to know photocatalytic properties of tio2 nanoparticles...what to do now
it is a goid question and i want to know the answer as well
Maciej
Abigail
for teaching engĺish at school how nano technology help us
Anassong
Do somebody tell me a best nano engineering book for beginners?
there is no specific books for beginners but there is book called principle of nanotechnology
NANO
what is fullerene does it is used to make bukky balls
are you nano engineer ?
s.
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
Tarell
what is the actual application of fullerenes nowadays?
Damian
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
Tarell
what is the Synthesis, properties,and applications of carbon nano chemistry
Mostly, they use nano carbon for electronics and for materials to be strengthened.
Virgil
is Bucky paper clear?
CYNTHIA
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
NANO
so some one know about replacing silicon atom with phosphorous in semiconductors device?
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Harper
Do you know which machine is used to that process?
s.
how to fabricate graphene ink ?
for screen printed electrodes ?
SUYASH
What is lattice structure?
of graphene you mean?
Ebrahim
or in general
Ebrahim
in general
s.
Graphene has a hexagonal structure
tahir
On having this app for quite a bit time, Haven't realised there's a chat room in it.
Cied
what is biological synthesis of nanoparticles
how did you get the value of 2000N.What calculations are needed to arrive at it
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Good
Berger describes sociologists as concerned with
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