Difference between revisions of "TRNAscan-Se"
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| − | tRNA detection in large-scale genome sequences. | + | tRNA detection in large-scale genome sequences.<br /> |
| − | 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. | ||
Revision as of 16:14, 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)