Quasar - Scoring and Ranking of Sequence-Structure Alignments

Birzele, Fabian
Gewehr, Jan Erik

Quasar is a platform-independent and easily extendable software package for scoring and ranking sequence-structure alignments. It also aids the process of developing and benchmarking new alignment scores. Besides using standard scoring functions, a user can easily add new alignment scores (so-called scoring schemes) and combine several scoring schemes in a scoring function by using a so-called score conductor. Such user-defined scoring functions may be used to rank a given set of sequence-structure alignments and benchmark the resulting ranking against a standard-of-truth ranking generated on the basis of one or more structure-based benchmark scores. Quasar also offers algorithms for optimizing combinations of scoring schemes with respect to the correlation with the benchmark score.

To allow users to take full advantage of the manifold possibilities that are offered by Quasar you can find a detailed tutorial on Quasar here. The tutorial is also available from the Quasar graphical user interface under the menu item "Help" and as a set of pdf-files for printing.

The Java Documentation which might be useful for developers can be found here

Users new to QUASAR that have Java web start installed on their system, can start the graphical user interface of QUASAR via this link. Please notice that you have to give the application the permission to write on your filesystem.

Notes

• If you have any problems with running the Web-Start version of QUASAR (in the Run, Benchmark or Optimization panels) please make sure that QUASAR may write temporary files to your directory system. You can select a directory where QUASAR may write files to in the menu bar under Properties -> Set Temporary Directory. If QUASAR is still not working properly feel free to contact us.
• Please notice that you can not change the virtual machine memory available for Quasar in the web start version. If you observe a java.lang.OutOfMemoryError: Java heap space exception while running Quasar please download the standalone version of the software and extend the memory available to the virtual machine (see tutorial for details).

Java Web start is included in the J2SE 5.0 distribution and can be downloaded from here.

Even though the Web-Start version has the full functionallity of the Quasar graphical user interface, we recommend downloading the standalone distribution of the software.

• Quasar v1.2: You can download the current version (1.2) of QUASAR here. Since the method is still being under development, please check back from time to time to see if any updates are available. The file contains the software, matrices, examples and the full documentation (Java Documentation and tutorial).
• Matrix files: All matrix files available so far can be downloaded here.
• Tutorial: *.pdf files of the tutorial pages are available here

example.config	Exemplary QUASAR configuration file containing a weighted sum score conductor.
pam250.mat	The PAM250 matrix in a format similar to the format used by the AAIndex database.
treeconfig.config	Exemplary benchmark configuration file containing a formula tree score conductor.
globin.align	Exemplary collection of alignments between globins. The format is as follows: Alignments start with a header: "> " + templatename + " " + targetname + " | " + user-defined benchmark score. Then four lines follow: QA is followed by the query amino acid sequence, TA by the template amino acid sequence, QS by the query secondary structure sequence (three-state) and TS by the template secondary structure sequence. After each alignment there is a blank line.
globin.align.ranking	Exemplary ranking output for a combination of the PAM250 and the Q3 score. The template structure files are shown together with the results of the different scoring schemes and benchmark scores.

For a description of these files, please have a look at the tutorial.

If you used QUASAR for your own research, please cite: