About GFF files

The .gff and .fasta files located in the files download area of the GMOD web site correspond to feature and dna information for the model organism systems drosophila, C. elegans, and yeast. They are designed to be loaded into the Generic Genome Browser (GBrowse) for browsing. You can think of them as a starter's kit for your own genome browser.

These files are *not* necessarily kept up to date, but are imported from the model organism databases at irregular intervals. You are strongly advised to generate your own versions of these files if you want the most current data.

To assist in updating, the GBrowse distribution comes with several scripts for converting the data downloaded from the model organism databases into .gff format. These are:

process_wormbase.pl	   Import C. elegans annotations from WormBase
process_sgd.pl           Import S. cerevisiae annotations from SGD
process_gadfly.pl        Import D. melanogaster annotations from Flybase

Here is a brief description of the process for importing these files:

1. WormBase

The GFF files distributed at WormBase are actually useable as is. The process_wormbase.pl script adds some useful information to the GFF files, most notably the positions of genetically mapped genes. However you will need the Ace module (available at http://www.cpan.org) to use it.

a)

Go to ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS/ and download the CHROMOSOME_?.gff.gz files that you find there. Put them all into one local directory named "wormbase_orig".

b)

While you're there, go to ftp://www.wormbase.org/pub/wormbase/DNA_DUMPS/unpacked and download the six CHROMOSOME_?.fa files that you find there. Put them into wormbase_orig too.

c)

Create a new directory called wormbase_new".

d)

Convert the WormBase GFF files into gbrowse GFF files:

process_wormbase.pl wormbase_orig > wormbase_new/wormbase.gff

e)

Copy the DNA files to wormbase_new

mv wormbase_orig/*.fa wormbase_new

f)

Load everything -- see gbrowse instructions for how this works.

fast_load_gff.pl -d elegans -f wormbase_new wormbase_new/wormbase.gff

2. FlyBase

The FlyBase files are maintained in a Berkeley database called GadFly. They must be processed before they can be used in gbrowse.

a)

Go to ftp://ftp.fruitfly.org/pub/genomic/gadfly/ and download the files named RELEASEXXgff.2L.tar.gz, RELEASEXXgff.3L.tar.gz and so on, where XX corresponds to the latest release. These are annotation files.

b)

Go to ftp://ftp.fruitfly.org/pub/genomic/fasta/ and get the file na_arms.dros.RELEASEXX.Z. This contains the sequence in FASTA format. Make sure to use the same release number as the annotation files!

c)

Unpack the annotation files to yield a directory named after the release, e.g. RELEASE2, containing a directory named after the chromosome arm. Do this repeatedly in order to create a directory that contains each of the chromosome arms, i.e.:

RELEASE2/gff/X
RELEASE2/gff/2L
RELEASE2/gff/2R

d)

Run the process_gadfly.pl script to convert into gbrowse GFF format:

process_gadfly.pl ./RELEASE2 > fly.gff

e)

Run the following script to put the fly FASTA files into a loadable format:

uncompress -c na_arms.dros.RELEASEXX.Z  | \
     perl -pe 's/^>Chromosome_arm_(S+)/>/' > fly.fa

f)

Run the GFF loader

fast_load_gff.pl -d fly -f fly.fa fly.gff

3. SGD (yeast)

a)

Go to ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/ and download the files chromosomal_feature.tab.

b)

Go to ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/chromosomes/fasta and download all the .fsa files.

c)

Run the process_sgd.pl script to create a loadable GFF file.

process_sgd.pl chromosomal_features.tab > yeast.gff

d)

Run the following script to put the FASTA files into a loadable format:

perl -pe 's/>.+chromosome=(\w+)/>$1//' *.fsa > yeast.fa

e)

Run the GFF loader

fast_load_gff.pl -d yeast -f yeast.fa yeast.gff

IMPORTANT NOTE:

File formats and paths change all the time. These recipes worked as of 11/07/02, but are not guaranteed for the future!