BIGNASim database structure and analysis portal for nucleic acids simulation data
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.
As a quick example, we show here the generation of a meta-trajectory of one of the tetramers having less occurrences (ACGT, 4 occurrences). The same procedure could be used to generate meta-trajectories for all of the possible tetranucleotides including CG, thus obtaining a valuable set of ensembles to analyse and compare. The first step of the procedure consists on accessing the search section of the portal from the main menu (see Case example 1), to locate simulations of normal duplex B-DNA systems containing ACGT.
Results for this specific search are 3 simulations. The information that we will constitute the final meta-trajectory is the combination of all the selected trajectories, 1.290µs (500 + 500 + 290 ns). Note that if the most represented tetramer including CG (TCGC) was chosen, the generated meta-trajectory would correspond to up to 39 µs of simulated time, so this option should be used with care. Meta-trajectory can be obtained from the "Retrieve Metatrajectory" button, after selecting the appropriate simulations.
The next step for generating the meta-trajectory is to define a desired frame step. In this case, 100 snapshots as representatives of each trajectory will be extracted (Frame input section: 1:5000:50 (for snapshot 1 to snapshot 5000, every 50 snapshots). At this step, trajectory can be downloaded or sent to NAFlex nucleic acid flexibility server.
As the generation of the trajectory is potentially a lengthy process, a temporary private user space is created where downloaded trajectories or meta-trajectories are maintained.
