25-07-2012, 01:04 PM
The 2D Gel Electrophoresis Simulator
[attachment=28867]
Introduction
2-dimensional (2D) gel electrophoresis has been a popular and useful protein/DNA analysis method
for a long time because of its ease of examination. Although the procedure of this method is relatively
easier than other molecular biological experiments, it has several physically caused limitations such as
randomdistortion of gel, spot smears and quasi-spots (artifacts), and uneven intensity of each spot.
In order to alleviate these difficulties and help practitioners with computational aids, we developed
the SimGel, an interactive 2D gel electrophoresis simulator. SimGel helps you to analyze ordinary
electrophoresis quantitatively, interactively, and in details of single nucleotide/amino-acid of every
spot with pin-point accuracy.
SimGel allows practitioners to:
• try many kind of restriction enzymes and examine optimal experimented condition in advance
• pin-point the approximate location of the focused spots
• view the location of spots without any smear and gel distortion
• trace the location of spots(labeled/unlabeled) in arbitrary time-scale and physical scale
• measure the spots in one nucleotide/amino-acid wise
• review the nucleotide/amino-acid sequence interactively
So we believe that this new application programwill not only help practitioners of molecular
biological experiment but also change the way to practice the experiments in biology laboratory. And
additionally, combination of SimGel and automated RLGS (Restriction Landmark Genomic Scanning)
electrophoretogram processing method [1] will promote the highly computational functional analysis
of genes that is very crucial for post-Genome Project research activities.
Method and Results
2D gel electrophoresis simulation naturally requires the modeling of behavior of molecules in a gel
with electoric potential gradient. Simulation of protein electrophoresis needs prediction of isoelectric
points, denoted as pI, for every tested proteins. Although the prediction of pI is expected to be built
in SimGel, current implementation employs simulation of DNA electrophoresis only. We wanted to
find mobility dependency on molecular size to compute the location of every spot at arbitrary moment.
We measured the mobility of every spot that has different molecular size from our examination results
of electrophoresis for E. coli genome. As Figure 2 shows, the measurement found that, in a certain
range of molecular size (m), the mobility (M) can be denoted in the equation; M(m) = expa log(m)+b.
However too small/large molecules do not follow the equation and such molecules are almost invisible
on the electrophoretogram.
[attachment=28867]
Introduction
2-dimensional (2D) gel electrophoresis has been a popular and useful protein/DNA analysis method
for a long time because of its ease of examination. Although the procedure of this method is relatively
easier than other molecular biological experiments, it has several physically caused limitations such as
randomdistortion of gel, spot smears and quasi-spots (artifacts), and uneven intensity of each spot.
In order to alleviate these difficulties and help practitioners with computational aids, we developed
the SimGel, an interactive 2D gel electrophoresis simulator. SimGel helps you to analyze ordinary
electrophoresis quantitatively, interactively, and in details of single nucleotide/amino-acid of every
spot with pin-point accuracy.
SimGel allows practitioners to:
• try many kind of restriction enzymes and examine optimal experimented condition in advance
• pin-point the approximate location of the focused spots
• view the location of spots without any smear and gel distortion
• trace the location of spots(labeled/unlabeled) in arbitrary time-scale and physical scale
• measure the spots in one nucleotide/amino-acid wise
• review the nucleotide/amino-acid sequence interactively
So we believe that this new application programwill not only help practitioners of molecular
biological experiment but also change the way to practice the experiments in biology laboratory. And
additionally, combination of SimGel and automated RLGS (Restriction Landmark Genomic Scanning)
electrophoretogram processing method [1] will promote the highly computational functional analysis
of genes that is very crucial for post-Genome Project research activities.
Method and Results
2D gel electrophoresis simulation naturally requires the modeling of behavior of molecules in a gel
with electoric potential gradient. Simulation of protein electrophoresis needs prediction of isoelectric
points, denoted as pI, for every tested proteins. Although the prediction of pI is expected to be built
in SimGel, current implementation employs simulation of DNA electrophoresis only. We wanted to
find mobility dependency on molecular size to compute the location of every spot at arbitrary moment.
We measured the mobility of every spot that has different molecular size from our examination results
of electrophoresis for E. coli genome. As Figure 2 shows, the measurement found that, in a certain
range of molecular size (m), the mobility (M) can be denoted in the equation; M(m) = expa log(m)+b.
However too small/large molecules do not follow the equation and such molecules are almost invisible
on the electrophoretogram.