Information Technology Reference
In-Depth Information
A
B
Figure 7
: Region of 74 kb around the switching point of chromosome 21 of
L. major
. L7171 and L3640 are two cosmids containing the overlapping
fragments of chromosome 21. The two strands and the encoded genes are
represented in different colors. The curvature analysis of the 40 kb around
the switch region is shown in the lower window.
3. The DNA-analysis tools developed at ICGEB
The plot.it server
produces parametric plots using various statistical
physicochemical parameters [31]. A query sequence is divided into overlapping n-mers,
and the average value of a given parameter is calculated using tabulated values. The server
uses 45 structural parameters (a full list of references is available at the site), the general
scheme of calculations is shown in
Figure 3
. The results appear either as simple sequence
plots or as 2-D plots in which two parameters are plotted against each other. Examples are
shown in
Figure 4
.
The bend.it server
calculates the curvature of DNA molecules as predicted from the
DNA sequences. The calculation is based on values tabulated for dinucleotides and
trinucleotides, and the curvature (degree per helical turn) is calculated using standard
algorithms [9]. This calculation was originally based on DNA bendability parameters
derived from DNAseI digestion that characterize the (static or dynamic) bending of
trinucleotides towards the major groove [2]. Today a number of other dinucleotide [32-34]
and trinucleotide models [2, 4] are included, and the results can be visualized as 1D or 2D
plots on the screen. Both the bend.it and the plot.it servers are based on C programs
provided with GnuPlot graphic routines. Their output appears on the screen and is
optionally sent by e-mail to the user (
Figure 5
).
The model.it server
was designed to provide 3D models of DNA in response to
DNA sequence queries [35]. The results are presented as a standard PDB file that can be
viewed directly using any of the widely available molecule manipulation programs such as
Swiss-PDBviewer [36] or Rasmol [37]. In addition to straight A and B DNA models, the
server is capable of building curved DNA models using the parameter sets mentioned
