Information Technology Reference
In-Depth Information
parametric genome maps are available in the Genome Atlas of the Technical University of
Denmark [29, 30].
ATGACGTAATAATGC...
(SEQUENCE)
plot.it
bend.it
model.it
AAA 0.1
AAC 1.6
AAA 0.1
AAC 1.6
...
...
(PARAMETER SET)
Figure 3.:
Data flow of the bend.it, plot.it and model.it servers. Each overlapping
triplet (or dinucleotide) in a DNA sequence is assigned a corresponding parameter
value in a “sliding window” fashion. The resulting numerical vector can then be
averaged within a given window (default value is 31bp or approximately three
helical turns) and displayed either as a 1C parameter vs. sequence plot, or as a 2D
correlation plot from two different parameter sets. (Three-dimensional DNA
trajectories are built from basepair geometry parameters without averaging).
F
igure 4.
Output examples of the plot.it server. A three-dimensional correlation
plot of the
Anadara trapezia
(ark clam) beta globin gene (complete cds.
genbank:L16978). The vertical Z-axis denotes the number of actual segments
represented by data on the XY plane. This type of correlation plot is useful in
situations where analysis is performed on a long DNA sequence
