| |
|
|
|
|
| ChemGenome - A Physico-chemical
Model for Genome Analysis |
|
|
Chemgenome is based on the hypothesis that
both the structure of the DNA and its interactions with
regulatory proteins and polymerases decide the function of a
DNA sequence. It uses a simple three-parameter model based on
Watson-Crick hydrogen-bonding energy, base-pair stacking
energy, and a third parameter which is related to
Protein-Nucleic Acid interactions. Each of these parameters
acts as a dimension for a three-dimensional unit vector, whose
orientation differs for each trinucleotide.
|
|
DNA sequence is made up of set of four bases
(A, T, G, C) which combine in different possible manner to give
64 unique codons. Each of the 64 codons(trinucleotides) are
assigned a X(Hydrogen Bonding Energy), Y(Stacking Energy) and
Z(protein-Nucleic acid interaction).
-
The first component was constructed by
finding the Hydrogen bonding energy of
trinucleotides(codons).
-
The second component was constructed by
finding the Stacking energy(sum of electrostatic,
hydrophobic and other forces which the trinucleotides are
exposed to when it is stacked with other nucleotides in the
B-DNA form).
-
|
|
|
Every sequence is broken down into
trinucleotides, the three components for each trinucleotide
are added up. The values assigned to all the trinucleotides
are normalized to lie in the range [-1,1]. These unit vectors
are then plotted on unit spheres.
A physical separation of the vectors
corresponding to coding DNA sequences and the non-coding DNA
sequences was observed by plotting them as dots on a 3D plane. All
the coding DNA sequences are represented as blue dots while the
non-coding DNA sequences are represented as red dots. |
|
| This physical separation of the vectors
corresponding to genes and non-genes is the basis of the
physico-chemical model of Gene Evaluation. Once the best
separating plane is obtained, we only need to check if the new
DNA sequence lies on the Gene side of the plane or the other
side. |
Physico-chemical evaluation has proven accurate for Prokaryotes
to an accuracy of >95% and forms the basis of Chemgenome
1.1.
|
S.No. |
NCBI_ID |
Species Name |
Genes |
TP# |
FP# |
SS# |
SP# |
CC# |
1 |
NC_000117 |
Chlamydia trachomatis |
463 |
458 |
4 |
0.98 |
0.99 |
0.98 |
2 |
NC_000853 |
Thermotoga maritima MSB8 |
641 |
619 |
3 |
0.96 |
0.99 |
0.96 |
3 |
NC_000854 |
Aeropyrum pernix K1 |
561 |
532 |
7 |
0.94 |
0.98 |
0.93 |
4 |
NC_000868 |
Pyrococcus abyssi GE5 |
632 |
630 |
241 |
0.99 |
0.63 |
0.49 |
5 |
NC_000907 |
Haemophilus influenzae |
955 |
953 |
7 |
0.99 |
0.99 |
0.99 |
6 |
NC_000908 |
Mycoplasma genitalium G-37 |
189 |
186 |
2 |
0.98 |
0.98 |
0.97 |
7 |
NC_000909 |
Methanocaldococcus janaschii |
720 |
708 |
9 |
0.98 |
0.98 |
0.97 |
8 |
NC_000912 |
Mycoplasma pneumoniae M129 |
243 |
241 |
2 |
0.99 |
0.99 |
0.98 |
10 |
NC_000915 |
Helicobacter pylori |
731 |
727 |
4 |
0.99 |
0.99 |
0.98 |
11 |
NC_000916 |
Methanobacterium thermoautotrophicum |
719 |
711 |
4 |
0.98 |
0.99 |
0.98 |
12 |
NC_000917 |
Archaeoglobus fulgidus |
782 |
774 |
8 |
0.98 |
0.98 |
0.97 |
13 |
NC_000917 |
Archaeoglobus fulgidus DSM4304 |
782 |
774 |
8 |
0.98 |
0.98 |
0.98 |
14 |
NC_000918 |
Aquifex aeolicus VF5 |
584 |
575 |
3 |
0.98 |
0.99 |
0.97 |
15 |
NC_000921 |
Helicobacter pylori strain J99 |
658 |
648 |
9 |
0.98 |
0.98 |
0.97 |
16 |
NC_000922 |
Chlamydophila pneumoniae CWL029 |
597 |
590 |
9 |
0.98 |
0.98 |
0.97 |
17 |
NC_000948 |
Borrelia burgdorferi B31 plsmids cp32-1 |
11 |
11 |
0 |
1.0 |
1.0 |
1.0 |
18 |
NC_000949 |
Borrelia burgdorferi B31 plsmids cp32-3 |
11 |
11 |
0 |
1.0 |
1.0 |
1.0 |
19 |
NC_000950 |
Borrelia burgdorferi B31 plsmids cp32-4 |
11 |
11 |
0 |
1.0 |
1.0 |
1.0 |
20 |
NC_000951 |
Borrelia burgdorferi B31 plsmids cp32-6 |
10 |
10 |
0 |
1.0 |
1.0 |
1.0 |
Chemgenome 2.0 goes a step further and
predicts the coding regions in Prokaryotes if a whole genome
or part of genome is given as an input.
To know more about this physico-chemical
model, refer to
References |
[1]
Progenie "Decoding the Design Principles of Amino Acids and the Chemical Logic of Protein Sequences", Jayaram, B. Available from Nature Precedings. http://hdl.handle.net/10101/npre.2008.2135.1 2008 Read Paper
|
[2]"Prokaryotic Gene Finding based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations", Singhal P, Jayaram B, Dixit S B and Beveridge D L, Biophys. J. ,2008, 94(11), 4173-4183. [ Read Paper ]
|
[3] "A Physico-Chemical
model for analyzing DNA sequences", Dutta S, Singhal P,
Agrawal P, Tomer R, Kritee, Khurana E and Jayaram B,
J.Chem. Inf. Mod., 2006, 46(1), 78-85.[ ABSTRACT ].
|
[4] "Beyond the Wobble :
The rule of conjugates", Jayaram B, Journal of Mol.
Evol., 1997,45,704-705.
|
|
| |
