View source for TWINSCAN

[[Category:Software]][[Category:biology]][[Category:genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|twinscan}}
|{{#vardefine:url|http://mblab.wustl.edu/software.html#twinscanLink}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
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<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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)

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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* TWINSCAN - twinscan variable for base directory

<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#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.

|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} 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

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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