PTRStalker is an algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. The name of the tool is inspired by Tarkovsky’s Stalker movie.
PTRStalker detects tandem repeats by:
- finding a set of candidate periods;
- finding a set of candidate pairs (period, starting position);
- verifying if in a particular position there exists a tandem repeat according to the precise mathematical definition adopted.
The use of BLOSUM based metrics within PTRStalker is effective in detecting long fuzzy tandem repeats. More in general, PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences with performance beyond the current state-of-the art.
PTRStalker allows you to:
- import a new sequence from a file in fasta format or from the UniProt database;
- analyze a sequence and store the results on a local database;
- retrieve these results at a different time for further investigation.
By launching PTRStalker, you can:
- import a new sequence into the local database;
- start the analysis of a sequence that is already in the local database;
- load an analysis previously saved into the local database;
- change the algorithm parameters;
- manage the local database, by deleting a saved sequence (and all the analyses associated), or a saved analysis, or the whole local database.
In order to analyze a new sequence you have to import it into the local database. A new sequence can be imported in PTRStalker by uploading a local file in fasta format, or from the UniProt remote database by providing the accession number (due to changes in the remote service, the latter functionality is currently unavailable).
If the file is multi-fasta, multiple sequences are imported into the local DB with a single operation.
Once the sequence has been imported, you can go back and chose to analyze one of the sequences imported in the local database. When the analysis is complete, save it and view the results. You can also re-load a previously saved analysis.
In the result window, you can visualize:
- the summary, with details on the submitted sequence, the parameters used for running PTRStalker, and the tandem repeats the algorithm found in the submitted sequence; and
- the detailed results, where you can analyze the tandem repeats found, the alignment, and re-compute the score by changing the input parameters.
Running PTRStalker
PTRStalker used to run by means of Java Web Start. Oracle has discontinued the latter but you can now use OpenWebStart, which provides similar functionalities.
PRTStalker is known to work with OpenWebStart 1.8 + Java 11 (so you also need to install Java 11 if it is not already installed on your system). You can configure the JVM to be used by means of the JVM Manager panel in the OpenWebStart configuration GUI:
Once you configured OpenWebStart, just click here to download the JNLP file. Then just open the JNLP file to start the application.