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above. The server program was written using "NAB" - a high level molecule manipulation
language [38]. Coordinates of the sugar-phosphate backbone are optionally optimised with
constrained molecular dynamics using energy parameters from the AMBER package [39].
At present, the server can produce models of 700 bp in length, but models longer than 50
bp will not be optimised. Modelling of canonical, straight B or A DNA structures proceeds
in a similar way, but without the need for backbone geometry optimisation ( Figure 6 ).
The IS introns server was designed to provide statistical overviews on intron
groups [40]. Simple questions, like comparison of introns between various taxonomic
groups in terms of intron phases or size-distributions as well as the analysis of splice sites,
requires a carefully selected dataset as well as meticulous work that has to be repeated as
new data become available. The goal of the introns server was to establish an automatically
updated intron resource that allows the evaluation of experimentally validated and
statistically balanced intron datasets, as well as a flexible comparison of groups according
to various criteria. In addition to sequence retrieval and BLAST similarity search, there are
options to compare taxonomic groups based on the NCBI Taxonomy Database, and to
perform on the fly statistics. The analysis capabilities of the IS server include statistical
evaluation (minimum, maximum, average, standard deviation, etc.) of intron and exon
length, of the number of introns per gene, base composition, intron phases, as well as a
graphic comparison of two or more groups in terms of the above variables. In addition, the
analysis of splice sites and testing of the exon shuffling hypothesis [41, 42] are explicitly
included ( Figure 7 ).
All the servers are provided with help files that describe the detailed instructions,
the theory, the literature citations as well as the instructions for installing the accessory
programs such as Swiss-PDBviewer [36] or Rasmol [37].
Bendability distribution
Curvature distribution
25
14
B. sub tilis
C. elegans
E. coli
H. influenzae
M. genitalium
M. janaschii
M. pneumoniae
S. cerevisiae
Synechocistis sp.
B. sub tilis
C. elegans
E. coli
H. influenzae
M. genitalium
M. janaschii
M. pneumoniae
S. cerevisiae
Synechocistis sp.
12
20
10
15
8
6
10
4
5
2
0
0
0
1
2
3
4
5
6
7
8
9
10
0
2
4
6
8
10
12
14
16
18
20
Bendability (a.u.)
Curvature (degree/helical turn)
F igure 8. Distribution of bendability and curvature in various prokaryotic genomes
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