GBrowse – Introduction

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

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Human Genome Segmental Duplication Database GBrowse – Examples

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

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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

GBrowse – Introduction