Perl scripts to analyze tRNA gene content, codon frequency and their correlation in genomes.
BASED on:
- tRNAscan-SE Lowe, T.M. & Chan, P.P. (2016) Nucl. Acids Res. 44: W54-57.
Lowe, T.M. & Eddy, S.R. (1997) Nucl. Acids Res. 25: 955-964.
- CodonW 1.4.4 http://codonw.sourceforge.net/
** SYSTEM REQUIREMENTS **
All scripts are written in Perl programming language. A Perl interpreter has to be installed.
tRNAscan-SE binaries are compiled for UNIX machines so you need UNIX-based OS or CygWin for Windows OS.
MANDATORY
- Install a Perl interpreter OPTIONAL Add Bribes and Trouchelle repositories:
- ppm rep add Bribes http://www.bribes.org/perl/ppm
- ppm rep add Trouchelle http://trouchelle.com/ppm
- Install the following Perl modules:
- List::Util
- LWP
- Statistics::RankCorrelation
- Statistics::Distributions
- Statistics::R (at least version 0.33)
OPTIONAL To use all the features of CORR checker
- Install R:
- Install the package "coin".