Difference between revisions of "TRNAscan-Se"

From UFRC
Jump to navigation Jump to search
 
(7 intermediate revisions by 3 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:biology]][[Category:bioinformatics]][[Category:ngs]]
+
[[Category:Software]][[Category:biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|trnascan-se}}
 
|{{#vardefine:app|trnascan-se}}
Line 18: Line 18:
 
{{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.<br />
+
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.
 +
 
  
  
    tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes,<br />
 
with a false positive rate of less than one per 15 gigabases, and with a <br />
 
search speed of about 30 kb/second. It was implemented for large-scale human <br />
 
genome sequence analysis, but is applicable to other DNAs as well. It <br />
 
applies our COVE software (see below) with a carefully built tRNA covariance <br />
 
model, while getting around COVE's speed limitations by using two tRNA <br />
 
finding programs from other research groups as fast first-pass scanners <br />
 
(Fichant and Burks', and an implementation of an algorithm from A. Pavesi's <br />
 
group). It runs on any UNIX system with Perl and a C compiler installed.
 
  
  
Line 36: Line 28:
 
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_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
+
* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
  
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 20:53, 12 August 2022

Description

trnascan-se website  

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)