Download - GBrowse – Introduction
GBrowse – Introduction
Developed by GMODGeneric 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 GenomeSegmental DuplicationDatabase
GBrowse – Features
banner
description
tracks
cookies
instructions
search
overview
details
overview
region displayed
GBrowse – Features what’s
allowablefor searches
bookmark current view and settings
for re-visits to page
view Detail image in SVG format
restore standardsettings
GBrowse – Features
Gene symbolsGene IDsSequence IDsGenetic markersRelative nucleotide coordinatesAbsolute nucleotide coordinatesetc...
click
GBrowse – Features
pick-list
GBrowse – Installation
Apache
MySQL (recommended)
Perl
Standard Perl modulesCGI (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)
BioPerlBio::Graphics Bio::DB::Das::Chado
Optional Perl modulesXML::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/
GBrowse – Installation
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