Transcript Slide 1

GBrowse – Introduction
Developed by GMOD
Generic Model Organism Database
Generic Genome Browser
Web application to explore genomes
Free software
Goal: simplify & standardize MODs
Model Organism Databases
GBrowse – Introduction
bird’s eye view...
...or zoom in
for details
colored glyphs
customize it
GBrowse – Examples
Human Genome
Segmental Duplication
Database
GBrowse – Features
banner
description
instructions
search
overview
details
tracks
cookies
region displayed
GBrowse – Features
what’s
allowable
for searches
restore standard
bookmark current
view Detail image settings
view and settings
in SVG format
for re-visits to page
GBrowse – Features
click
Gene symbols
Gene IDs
Sequence IDs
Genetic markers
Relative nucleotide coordinates
Absolute nucleotide coordinates
etc...
GBrowse – Features
pick-list
GBrowse – Installation
Apache
MySQL (recommended)
Perl
Standard Perl modules
CGI (2.56 or higher)
GD (2.07 or higher)
CGI::Session (4.03 or higher)
DBI (any version)
DBD::mysql (any version)
Digest::MD5 (any version)
Text::Shellwords (any version)
Class::Base (any version)
GBrowse – Installation
BioPerl
Bio::Graphics
Bio::DB::Das::Chado
Optional Perl modules
XML::Parser, XML::Writer, XML::Twig, XML::DOM
LWP
Bio::Das
BioMOBY
GD::SVG
Bio::SCF File::Temp io-lib(v1.7+)
Math::FFT Statistics::Descriptive
Bio::PrimerDesigner, Math::Round, primer3
GBrowse – Installation
http://prdownloads.sourceforge.net/gmod
File: GBrowse-2.21.tar.gz
Extract: tar –xvzf GBrowse-2.21.tar.gz
Folder: cd GBrowse-2.21
GBrowse – Installation
http://prdownloads.sourceforge.net/gmod
File: GBrowse-2.21.tar.gz
Extract: tar –xvzf GBrowse-2.21.tar.gz
Folder: cd GBrowse-2.21
Run in terminal for unix system
perl Makefile.PL
make
make test (optional)
make install
GBrowse – Installation
perl Makefile.PL
HTDOCS : /var/www/
CONF: /etc/apache2/
CGIBIN: /usr/lib/cgi-bin
APACHE: /var/www/
Database – Preparations
mysql -uroot -ppassword -e 'create database yeast'
mysql -uroot -ppassword -e 'grant all privileges on yeast.* to
me@localhost‘
mysql -uroot -ppassword -e 'grant file on *.* to me@localhost'
mysql -uroot -ppassword -e 'grant select on yeast.* to nobody@localhost‘
bp_bulk_load_gff.pl -d yeast –create sample_data/yeast_data.gff
bp_load_gff.pl -d yeast -fasta yeast.fasta.gz
bp_bulk_load_gff.pl -d yeast sample_data/yeast_data.gff
GBrowse – Configuration
[GENERAL]
description = S. cerevisiae (via SGD Nov 2001)
db_adaptor = Bio::DB::GFF
db_args = -adaptor dbi::mysql
-dsn dbi:mysql:database=yeast;host=localhost
aggregators = transcript alignment
user =
passwd =
.
[Genes]
feature = gene:sgd
glyph = generic
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height = 6
description = 1
key = Named gene
GBrowse – Configuration
init_code = sub score_color {
my $feature = shift;
if ($feature->score > 50) {
return 'red';
} else{
return 'green';
}
}
sub score_height {
my $feature = shift;
if ($feature->score > 50) {
return 10;
} else {
return 5;
}
}
GBrowse – Configuration
[EST_ALIGNMENTS]
glyph = generic
bgcolor = \&score_color
height = \&score_height