Example 3. Obtaining a Meta-trajectory (xCGy fragment)
The example show the procedure to build a meta-trajectory containing a particular nucleotide fragment using the BIGNASim portal. The previous example has shown how to extract directly from the database the distribution of a particular helical parameter, recovering the Twist bimodality. However, one can be interested in study different properties, not pre-calculated in BIGNASim database. For that, there is the possibility to generate, download, or send to NAFlex server a meta-trajectory containing just the nucleotide fragment of interest. It is build joining together the cartesian coordinates from a set of selected simulations stored in our database enclosing the fragment. To illustrate the power of BIGNASim database, the DB is searched for the 16 possible tetramers including CG base-pair, going from 2 (TCGG) to 49 (TCGC) occurrences (see table below), in the present database release.
