Oct 26, 2015
README.txt for Supplementary Data package to Ardell and Hou (2015)

* Contents
  --------
** README.txt

This file.

** tCE-Nov5-2014.3.fas

tRNAdb-CE v.8 data reannotated for 3' ends (on the basis of codes in
the descriptions) and function using TFAM 1.4 with the Silva model
(provided in this supplement).

** silva.coveam

TFAM model file based on the analysis of Silva et al. (2006) for
reannotation of bacterial tRNA gene sequences with anticodon templates
CAT into the three classes: Met-elongators, fMet-initiators,
lysidinylated Ile-elongators.

** model_cca.pl

Perl script to generate the structural reannotation of 3’ends of
tRNAdb-CE v.8 data based on tRNAdb-CE v.8-annotated 5’ends using the
dynamic programming algorithm described in Ardell and Hou (2015). This
script takes Fasta data on standard input and augments it as Fasta
format to standard output. Along with bacterial and archaeal-specific
TFAM runs, this script is one of the steps required to generate the
provided file tCE-Nov5-2014.3.fas from tRNAdb-CE v.8 data. Please see
the file CCA-HEATMAP-TAX-BROWSER/cca_mss.html for a detailed
explanations of the “warnings” generated by this script, on how to use
them to compute whether a tRNA gene templates CCA, and for statistics
on reannotations.

** compute_heatmap.pl

Perl script to regenerate the javascript-based taxonomic
heatmap-browser from primary datafile tCE-Nov5-2014.3.fas. To do this,
use the command:

compute_heatmap.pl tCE-Nov5-2014.3.fas > CCA-HEATMAP-TAX-BROWSER/Ardell_Hou.html

To generate the input files to phyloT and iTol use the commands:

perl compute_heatmap.pl -I tCE-Nov5-2014.3.fas > NCBI_tax_IDs_data.txt
perl -F, -ane 'print "$F[0]\n";' NCBI_tax_IDs_data.txt > phyloT_input_NCBI_taxIDs.txt
perl -F, -ane 'print "$F[0],$F[3]\n" if (@F > 2);' NCBI_tax_IDs_data.txt > iTol_input_CCA_Ini.txt
perl -F, -ane 'print "$F[0],$F[2]\n" if (@F > 2);' NCBI_tax_IDs_data.txt > iTol_input_CCA_All.txt
perl -F, -ane 'print "$F[0],$F[1]\n" if (@F > 2);' NCBI_tax_IDs_data.txt > iTol_input_Genome_Size.txt

You must also add the NCBI Taxonomic IDs in the color definition file but
removing the prefix "INT"

perl -ne 'if (/INT(\d+)/){print "$1\n"}' iTol_color_definitions.txt >> NCBI_tax_IDs_data.txt

** iTol_color_definitions.txt

Color definitions for clades to generate Figure 1 in Ardell and Hou

** phyloT.tre

Phylogenetic tree of NCBI taxon IDs from NCBI Taxonomy used to upload to
iTol to generate Figure 1 in Ardell and Hou

** CCA-HEATMAP-TAX-BROWSER/

Directory containing javascript-based taxonomic heatmap-browser of the
manuscript results

*** Ardell_Hou.html

Open this file from wihin this directory using a javascript-capable
web browser. Tested in Safari 8.0.8 and Chrome 45.0.2454.99 (64-bit)

*** jQuery.js
*** jquery.treeTable.css
*** jquery.treeTable.js
*** toggle-collapse-dark.png
*** toggle-collapse-light.png
*** toggle-expand-dark.png
*** toggle-expand-light.png

These files need to be in the same directory as the Ardell_Hou.html file
when viewing that file for the taxonomic browser to work.