Won Cheol Yim wyim-pgl

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
[Augustus](http://bio

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)

	#!/usr/bin/perl
	my $file1 = $ARGV[0];
	my $file2 = $ARGV[1];
	open my $R, "<", $file1 or die ("Could not open $file!");
	open my $P, "<", $file2 or die ("Could not open $file!");

	my %data = ();

	while (my $Rline = <$R>) {
	$Rline =~ s/[\r\n]//g;

	import sys
	import time
	from Bio import Entrez

	Entrez.email = "[email protected]"
	if not Entrez.email:
	print "you must add your email address"
	sys.exit(2)

	# create an empty list we will fill with the gene names