QUASAR Tuturial - Basics

Quasar is a flexible tool for calculating quality scores of sequence-structure alignments. The main reason for its flexibility is that you do not have to write any additional Java code in order to combine single alignment quality scores (also called scoring schemes) to scoring function (done by score conductors) but you only have to provide the system a XML - like configuration file. In some detail the configuration file has to contain the following information:

  • Alignment parser information: where is the alignment file, which alignment parser should be used to parse the alignments, should pdb files be parsed and if so, where can they be found
  • Scoring information: Tells the system which score conductor should be used and which scoring schemes should be combined by the conductor. The scoring schemes often require additional information (like gap penalties for exchange matrix scoring schemes) which is also specified here.
  • Benchmark information: If you want to benchmark your scoring function against standard-of-truth quality scores like MaxSub, Touch or APDB, this section of the configuration file provides the system the information about the benchmark scores to be used together with their individual information.

Finally, using Quasar and all its functionalities is all about writing configuration files. Since it is not obvious for an user how to write valid configuration files, this can be done conviniently with help of the graphical user interface of Quasar. More information about the GUI can be found here. The interested user may find some details about the configuration file in the section about configuration tags.