Difference between revisions of "TRNAscan-Se"

Revision as of 16:17, 5 February 2018

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_{{#uppercase:trnascan-se}}_DIR - installation directory
HPC_{{#uppercase:trnascan-se}}_BIN - executable directory
HPC_{{#uppercase: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)

@@ Line 73: / Line 73: @@
 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)
 |}}