The document discusses interval position analysis (IPA), a method for analyzing DNA and RNA sequences. IPA calculates characteristics such as V, G, and g values based on the distances between similar elements in a sequence. The values of IPA characteristics are sensitive to the order of elements in a sequence. IPA can be used to construct phylogenetic trees and analyze local profiles of RNA sequences. Heap's law and rank distribution models are also discussed in relation to evaluating DNA segmentation.

1. Interval position analysis (IPA)
Common order
g=1.0308 ACCTTCATCCCCAACAAC
CACCACCATTACCACCAT
g=1.0462
g=1.0586 CACCACCATTACCACCTA
H=1.4591
IPA characteristics' values sensitive to the order of
elements in contrast to the characteristics of
Information theory (Claude Shannon)

2. Interval position analysis (IPA)
Special order
CT AGCT AGCT AGCT AGCT AGCT AGCT AGCT AG
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
H=2
g≈2
L→∞
g→H
If the special order of items in the sequence the values ​
of the characteristics of the IPA are approximately equal
to values of simular characteristics in Information theory
(Claude Shannon)

3. Ribosomal RNA
Shpynov S. N. (Proffessor, PHD) http://goo.gl/0XWsj
№ Organism g № Organism g
1 M.musculus 1,4174 16 Rattus norvegicus 1,4703
2 C.crocodylus 1,4186 17 Crocodylus niloticus 1,4784
3 C.familiaris 1,4280 18 I.persulcatus 1,4830
4 G.gallus 1,4284 19 Zebrias zebra 1,4907
5 Sus scrofa 1,4405 20 Kareius bicoloratus 1,4936
6 Amia calva 1,4409 21 O.moubata 1,4958
7 Homo sapiens 1,4429 22 P.humanus cap 1,5031
8 Th.thermophilus 1,4483 23 M.domestica 1,5110
9 Thermotoga thermarum 1,4483 24 S.pyogenes 1,5164
10 Gallus gallus 1,4557 25 B.anthracis 1,5221
11 Bos taurus 1,4607 26 B.burgdorferi 1,5222
12 Erinaceus europaeus 1,4636 Candidatus Nitrosopumilus
1,5239
13 Homo sapiens 1,4638 27 maritimus
14 Mus musculus 1,4656 28 M.pneumoniae 1,5329
15 Cricetulus griseus 1,4682 29 Neisseria gonorrhoeae 1,5353

4. Ribosomal RNA
Shpynov S. N. (Proffessor, PHD) http://goo.gl/0XWsj
g
Vertebrata Invertebrata Protozoa
Draft RNA analysis based on IPA (g) chart.

5. Phylogenetic trees made with ClustalW and method based on IPA (g)
IPA based
method
ClustalW

6. Local g profile
Local g profiles for 3 different organisms (Ribosomal RNA)
RNA length ≈ 1800
CACCACCATTACCACCAT window size = 100
step = 2 nucleotide

7. Evaluation of DNA segmentation based on the law
Heaps
Gnomic: A dictionary of genetic codes Pareto distribution http://goo.gl/PWu8B
Trifonov E, Brendel, V http://goo.gl/dZxJo Zipf’s Law http://goo.gl/Sjeum
Bradford’s law http://goo.gl/bdNjG
Heaps law http://goo.gl/u6H2F
CACCACCATTACCACCAT

8. Rank distribution
ln(nr) ln(Gr)
2 1
I II
3
ln(r ln(r
) )

9. Interval position analysis (IPA)
IPA characteristic based on distance between simular elements
N M M N V M V V N M N V
A L L A B L B B A L A B
F G G F H G H H F G F H
1 2 2 1 3 2 3 3 1 2 1 3
1 - - 1 - - - - 1 - 1 -
∆11 ∆12 ∆13 ∆14

10. Interval position analysis (IPA)
IPA characteristics
nj
m
V j =∏ Δ ij V =∏ V j
i=1
j=1
nj m nj
G j =∑ log 2 Δ ij G=∑ ∑ log 2 Δ ij
i =1 j =1 i=1
nj m
1 nj
g j = ∑ log Δ ij g =∑ log Δ gj
n j i=1 j=1 n
r= Δ g / D