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 tracks cookiesinstructions search overview details overview region displayed

GBrowse – Features what’s allowable for searches bookmark current view and settings for re-visits to page view Detail image in SVG format restore standard settings

GBrowse – Features Gene symbols Gene IDs Sequence IDs Genetic markers Relative nucleotide coordinates Absolute nucleotide coordinates etc... click

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)

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

File: GBrowse-2.21.tar.gz Extract:tar –xvzf GBrowse-2.21.tar.gz Folder: cd GBrowse-2.21 GBrowse – Installation

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 mysql -uroot -ppassword -e 'grant file on *.* to mysql -uroot -ppassword -e 'grant select on yeast.* to 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