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Open Access Highly Accessed Software

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

David Rosenkranz* and Hans Zischler

Author Affiliations

Institute of Anthropology, Johannes Gutenberg-University Mainz, Colonel-Kleinmann-Weg 2, 55099 Mainz, Germany

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BMC Bioinformatics 2012, 13:5  doi:10.1186/1471-2105-13-5

Published: 10 January 2012

Additional files

Additional file 1:

proTRAC output summary file that contains a list of all human piRNA clusters detected by proTRAC.

Format: TXT Size: 70KB Download file

Open Data

Additional file 2:

proTRAC output summary file that contains a list of all mouse piRNA clusters detected by proTRAC.

Format: TXT Size: 72KB Download file

Open Data

Additional file 3:

proTRAC output summary file that contains a list of all rat piRNA clusters detected by proTRAC.

Format: TXT Size: 71KB Download file

Open Data

Additional file 4:

proTRAC results folder containing a picture and a FASTA file for each detected human cluster. After decompression, the folder can be opened as former session in proTRAC. Alternatively, each file can be opened separately with any standard text-editor or graphic-viewer respectively.

Format: ZIP Size: 716KB Download file

Open Data

Additional file 5:

proTRAC results folder containing a picture and a FASTA file for each detected mouse cluster. After decompression, the folder can be opened as former session in proTRAC. Alternatively, each file can be opened separately with any standard text-editor or graphic-viewer respectively.

Format: ZIP Size: 1018KB Download file

Open Data

Additional file 6:

proTRAC results folder containing a picture and a FASTA file for each detected rat cluster. After decompression, the folder can be opened as former session in proTRAC. Alternatively, each file can be opened separately with any standard text-editor or graphic-viewer respectively.

Format: ZIP Size: 1.1MB Download file

Open Data

Additional file 7:

This document contains information on how the Macaca mulatta small RNA library was prepared and sequenced.

Format: DOC Size: 23KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 8:

proTRAC results folder containing a picture and a FASTA file for each detected macaca cluster. After decompression, the folder can be opened as former session in proTRAC. Alternatively, each file can be opened separately with any standard text-editor or graphic-viewer respectively.

Format: ZIP Size: 143KB Download file

Open Data

Additional file 9:

This folder contains the proTRAC software with all required files and a sample ELAND3 input file. The Perl script (proTRAC.pl) contains the source code of the software that can be run on any platform. Executing Perl scripts requires the installation of a Perl interpreter which is part of a standard Perl distribution like the freely available Strawberry Perl (http://strawberryperl.com/ webcite). Perl is preinstalled on most Macintosh and Linux systems. The folder also contains an executable file (proTRAC.exe) which runs on Windows systems without any further requirements.

Format: ZIP Size: 17MB Download file

Open Data