bp_process_gadflyp - Online in the Cloud

PROGRAM:

NAME

bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the
Generic Genome Browser

SYNOPSIS

% bp_process_gadfly.pl ./RELEASE2 > gadfly.gff

DESCRIPTION

This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/release3download.shtml into the "correct" version of the
GFF format.

To use this script, download the whole genome FASTA file and save it to disk. (The
downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give
the filename.) Do the same for the whole genome GFF annotation file (the saved file will
be called something like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
you wish you can download the ZIP compressed versions of these files.

Next run this script on the two files, indicating the name of the downloaded FASTA file
first, followed by the gff file:

% bp_process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff

The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:

% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff

(Where "fly" is the name of the database. Change it as appropriate. The database must
already exist and be writable by you!)

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

Component:arm A chromosome arm
Component:scaffold A chromosome scaffold (accession #)
Component:gap A gap in the assembly
clone:clonelocator A BAC clone
gene:gadfly A gene accession number
transcript:gadfly A transcript accession number
translation:gadfly A translation
codon:gadfly Significance unknown
exon:gadfly An exon
symbol:gadfly A classical gene symbol
similarity:blastn A BLASTN hit
similarity:blastx A BLASTX hit
similarity:sim4 EST->genome using SIM4
similarity:groupest EST->genome using GROUPEST
similarity:repeatmasker A repeat

IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not
work with earlier releases.

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