Difference between revisions of "TWINSCAN"
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| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
* TWINSCAN - twinscan variable for base directory | * TWINSCAN - twinscan variable for base directory | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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. | ||
|}} | |}} | ||
Latest revision as of 20:20, 27 May 2022
Description
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