The easiest way to search in BIGNASim server is using the Quick Search placed in the right part of the main menu tab. This form allows searching by PDB Id, ontology terms, keywords and authors.
In addition to the Quick Search, BIGNASim portal offers a powerful searching engine to find particular sequences/simulations. Basically, the search can be divided into three main sections:
Once the search is done, a browse page will appear showing the resulting trajectories.
The search engine is able to find a particular sequence, with the possibility to use regular expressions, which increases the power of the search. Input needed is just a chain of bases [A,C,T,G,U]. Examples:
Examples of interesting regular expressions could be:
Nucleic Acid sequence associated to a particular PDB file will be recovered if a PDB code is used as input in the Seq from PDB Code box. This allows to locate also other PDB entries sharing the same sequence or with small modifications.
One of the most important study to understand nucleic acids flexibility is applied in a base-pair step region. This section of the search engine allows to easily select a particular base-pair step to find all sequences simulated having this particular pair of nucleotides.
Typically, base-pair step studies omit terminal bases, to avoid fraying effects. For this reason, a flanking region (number of bases) can be given, and only those base-pair step having this number of bases before and after them will be retrieved.
All simulations stored in BIGNASim system are classified using a Nucleic Acids Ontology (see Ontology section).
The search engine is querying the database system on the fly, and showing the number of results found in the top-right corner of the ontology search box.
The ontology is split in 8 different sections: