RetroTector onlineRetroTector online has been moved to the new server and is now 10-20 times faster than in the original implementation.
This is a test version. It seems to work with most web browsers, but not all. If you get completely stuck, try another browser.
It can analyse any DNA sequence of length 5 - 10000 kB, preferably in FASTA or raw form (position numbers are OK). Please note that RetroTector is not at its best with sequences consisting of a provirus only; integration repeats and background DNA are valuable
To analyse, go to http://retrotector.neuro.uu.se/, paste data or select a sequence file, and click there relevant Send button. Then switch to Show queue and watch the progress. It may or may not make a difference if you now and then click the Refresh button or the browsers' Reload page or equivalent.
If the job is successful, download the result as a zip archive. You can view its contents with RetroTectorviewer, a double-clickable Java program (for obscure reasons, your browser might download RetroTectorviewer as RetroTectorviewer.zip. In that case, just rename it to RetroTectorviewer.jar). For this, you need to have a Java Runtime Environment (included in MacOS X, downloadable from java.sun.com for Windows). Just seek out the relevant file with Choose directory (which will also take you inside the zip archive). A rough understanding of what is displayed should be easy; to penetrate deeper you need to go to the RetroTector documentation, obtainable from Jonas.Blomberg@medsci.uu.se. A good starting point may be Chainview.html or RetroTector.html.
The present version of RetroTectorviewer (090310) has a couple of features not yet implemented in RetroTector: 1. it shows chunks with chains bold; this may take some time if there are many chunks. 2. if 'Manual marking' is checked, a section of a reading frame may be selected with two clicks and viewed.
The present version of RetroTector online is aimed primarily at primate genomes. Optimizations for other species will be implemented further on.