NAME

sgd_to_gff.pl - Massage SGD's feature dump format into a form suitable for Bio::DB::GFF

SYNOPSIS

perl sgd_to_gff.pl chromosomal_features.tab > sgd.gff

DESCRIPTION

This script massages the SGD yeast sequence feature file located at ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_feature.tab into a GFF format suitable for use with Bio::DB::GFF. This lets you view the yeast annotations with the generic genome browser (http://www.gmod.org).

To use this script, get the SGD features file at the above URL. Then run this command:

sgd_to_gff.pl chromosomal_feature.tab > sgd.gff

The resulting database will have the following feature types (represented as "method:source"):

Component:chromosome       A chromosome
gene:sgd                   A named gene
rRNA:sgd		     A ribosomal RNA
ARS:sgd		     An origin of replication
CEN:sgd		     Centromere
snRNA:sgd		     Small nuclear RNA
RNA:sgd		     An RNA gene
ORF:sgd		     An open reading frame
ORF|Pseudogene:sgd	     A probably pseudogene
LTR:sgd		     A long terminal repeat
Ty ORF:sgd		     ??
Transposon:sgd	     A transposon
Pseudogene|Ty ORF:sgd	     ??
snoRNA:sgd		     Small nucleolar RNA
tRNA:sgd		     Transfer RNA

AUTHOR

Lincoln Stein <lstein@cshl.org>