PTRStalker - Protein Tandem Repeats Discovery and Visualization

PTRStalker is a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences.   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. Download PTRStalker and get some help on using it.
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How to use PTRStalker
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. 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 analyse 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.
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References:
Ab initio detection of fuzzy amino acid tandem repeats in protein sequences Marco Pellegrini, M. Elena Renda, Alessio Vecchio BMC Bioinformatics 2012, Vol. 13(Suppl 3):S8, March 2012.
Detecting Fuzzy Amino Acid Tandem Repeats in Protein Sequences Marco Pellegrini, M. Elena Renda, Alessio Vecchio ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Chicago, USA. August 2011.
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