RetroTector
2021-05-04
• Download and uncompress the RetroTector package: ReTe1.0.1.zip
• See the included html documentation for setup
Quick start:
• Update full path to working directory in:
ReTe1.0.1/Database/Configuration.txt
• Start command (Mac/Unix) for RetroTector in the 'ReTe1.0.1/' directory:
java -Xmx1024m -classpath "RetroTector101.jar:." retrotector/RetroTector
• See the included html documentation for details:
ReTe1.0.1/Documentation/RetroTector.html
• Start analyzing:
- Place the fasta file(s) in ~/ReTe1.0.1/Workplace/NewDNA/
- Run "SweepDNA" from the RetroTector GUI "Execute" dropdown menu to process the fasta file(s) and generate folder(s) with script files in ~/ReTe1.0.1/Workplace/
- Process all scripts automatically by navigating to ~/ReTe1.0.1//Workplace/ in RetroTector GUI and run "SweepScripts" from the dropdown menu. This will process LTRID, ORFID and RetroVID in turn to generate results files.
- Navigate to the results folder(s) in RetroTector GUI and use "Choose script" to select the summarized results file "001SelectedChains.txt"
- Then "Execute script" in RetroTector GUI to view the results graphics
Please cite RetroTector in publications:
Sperber GO, Airola T, Jern P, Blomberg J.
Automated recognition of retroviral sequences in genomic data--RetroTector.
Nucleic Acids Res. 2007;35(15):4964-76.
doi: 10.1093/nar/gkm515
Correspondence: [email protected]