Ewan Birney


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


   perl sgd_to_gff.pl chromosomal_features.tab > sgd.gff


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


Lincoln Stein <lstein@cshl.org>