1BP_PROCESS_GADFLY(1)  User Contributed Perl Documentation BP_PROCESS_GADFLY(1)
2
3
4

NAME

6       process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version
7       suitable for the Generic Genome Browser
8

SYNOPSIS

10         % process_gadfly.pl ./RELEASE2 > gadfly.gff
11

DESCRIPTION

13       This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
14       http://www.fruitfly.org/sequence/release3download.shtml into the "cor‐
15       rect" version of the GFF format.
16
17       To use this script, download the whole genome FASTA file and save it to
18       disk.  (The downloaded file will be called something like
19       "na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML
20       page doesn't give the filename.)  Do the same for the whole genome GFF
21       annotation file (the saved file will be called something like
22       "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".)  If you
23       wish you can download the ZIP compressed versions of these files.
24
25       Next run this script on the two files, indicating the name of the down‐
26       loaded FASTA file first, followed by the gff file:
27
28        % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
29
30       The gadfly.gff file and the fasta file can now be loaded into a
31       Bio::DB::GFF database using the following command:
32
33         % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
34
35       (Where "fly" is the name of the database.  Change it as appropriate.
36       The database must already exist and be writable by you!)
37
38       The resulting database will have the following feature types (repre‐
39       sented as "method:source"):
40
41         Component:arm              A chromosome arm
42         Component:scaffold         A chromosome scaffold (accession #)
43         Component:gap              A gap in the assembly
44         clone:clonelocator         A BAC clone
45         gene:gadfly                A gene accession number
46         transcript:gadfly          A transcript accession number
47         translation:gadfly         A translation
48         codon:gadfly               Significance unknown
49         exon:gadfly                An exon
50         symbol:gadfly              A classical gene symbol
51         similarity:blastn          A BLASTN hit
52         similarity:blastx          A BLASTX hit
53         similarity:sim4            EST->genome using SIM4
54         similarity:groupest        EST->genome using GROUPEST
55         similarity:repeatmasker    A repeat
56
57       IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
58       files and will not work with earlier releases.
59

SEE ALSO

61       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
62

AUTHOR

64       Lincoln Stein, lstein@cshl.org
65
66       Copyright (c) 2002 Cold Spring Harbor Laboratory
67
68       This library is free software; you can redistribute it and/or modify it
69       under the same terms as Perl itself.  See DISCLAIMER.txt for dis‐
70       claimers of warranty.
71
72
73
74perl v5.8.8                       2007-05-07              BP_PROCESS_GADFLY(1)
Impressum