TWINSCAN

Description

twinscan website  

Twinscan/N-SCAN is our lab's suite of software for gene-structure prediction. We recommend running N-SCAN on our web server (http://mblab.wustl.edu/nscan). Twinscan is currently available for Mammals, Caenorhabditis (worm), Dicot plants, and Cryptococci. N-SCAN is available for human and Drosophila (fruitfly)

Environment Modules

Run module spider twinscan to find out what environment modules are available for this application.

System Variables

• HPC_TWINSCAN_DIR - installation directory
• HPC_TWINSCAN_BIN - executable directory
• TWINSCAN - twinscan variable for base directory

Additional Information

From TWINSCAN documentation:

In practice, Twinscan's memory requirements are approximately linear with the length of the target sequence. A rough guideline is 1 GB of memory for 1 Mb of input sequence.

See the sample nscandriver.config at /apps/twinscan/4.1.2/conf/nscandriver.config for details on how to set up a Nscan_driver.pl run.

Citation

If you publish research that uses twinscan you have to cite it as follows:

• Brent, M. R. (2008). Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nature Reviews Genetics, 9(1), 62-73. doi:10.1038/nrg2220
• Brent, M.R. (2007). How does eukaryotic gene prediction work? Nature Biotechnology. 25(8): 883-885.
• Gross, S. S., & Brent, M. R. (2006). Using multiple alignments to improve gene prediction. Journal of computational biology, 13(2), 379-393. doi:10.1089/cmb.2006.13.379