Difference between revisions of "TRNAscan-Se"
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| − | [[Category:Software]][[Category:biology]][[Category: | + | [[Category:Software]][[Category:biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|trnascan-se}} | |{{#vardefine:app|trnascan-se}} | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | tRNA detection in large-scale genome sequences. tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well. It applies our COVE software (see below) with a carefully built tRNA covariance model, while getting around COVE's speed limitations by using two tRNA finding programs from other research groups as fast first-pass scanners (Fichant and Burks', and an implementation of an algorithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed. | |
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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 |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
<!--Configuration--> | <!--Configuration--> | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | Lowe, T.M. and Chan, P.P. (2016) tRNAscan-SE On-line: Search and Contextual Analysis of Transfer RNA Genes. Nucl. Acids Res. 44: W54-57. | + | * Lowe, T.M. and Chan, P.P. (2016) tRNAscan-SE On-line: Search and Contextual Analysis of Transfer RNA Genes. Nucl. Acids Res. 44: W54-57. |
| − | Chan, P.P., Lin, B., and Lowe, T.M. tRNAscan-SE 2.0. (In Preparation) | + | * Chan, P.P., Lin, B., and Lowe, T.M. tRNAscan-SE 2.0. (In Preparation) |
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Latest revision as of 20:53, 12 August 2022
Description
tRNA detection in large-scale genome sequences. tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well. It applies our COVE software (see below) with a carefully built tRNA covariance model, while getting around COVE's speed limitations by using two tRNA finding programs from other research groups as fast first-pass scanners (Fichant and Burks', and an implementation of an algorithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed.
Environment Modules
Run module spider trnascan-se to find out what environment modules are available for this application.
System Variables
- HPC_TRNASCAN-SE_DIR - installation directory
- HPC_TRNASCAN-SE_BIN - executable directory
- HPC_TRNASCAN-SE_DOC - documentation directory
Citation
If you publish research that uses trnascan-se you have to cite it as follows:
- Lowe, T.M. and Chan, P.P. (2016) tRNAscan-SE On-line: Search and Contextual Analysis of Transfer RNA Genes. Nucl. Acids Res. 44: W54-57.
- Chan, P.P., Lin, B., and Lowe, T.M. tRNAscan-SE 2.0. (In Preparation)