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Advanced Bioinformatics Database Development with GBrowse and Chado Adaptors

This work presents a comprehensive overview of using GBrowse, a widely used web-based genome browser, in bioinformatics. The focus is on the application of multi-species comparative analysis and graphical representation of protein data utilizing the GUS and Chado database adaptors. Key features include live interactivity, customizable data tracks, and support for complex data types like synteny and protein data. Challenges include database tuning for improved performance and organization of configuration files for efficient project management.

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Advanced Bioinformatics Database Development with GBrowse and Chado Adaptors

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  1. GBrowse-related work at ApiDB Haiming Wang ApiDB Bioinformatics Resource Center Dr. Jessica Kissinger Group GMOD Nov 2007

  2. Same database schema – GUS • Multi-species – comparative analysis • Graphical for protein data

  3. Database adaptor vs GFF Pros: • Live interactive with database • Flexible with database schema – GUS, Chado • Support complex data type, e.g. synteny, protein data Cons: • Relatively slow – database tuning + bulkSubfeatures • Familiar with SQL

  4. Database Adaptor for GBrowse • Based on the Chado adaptor • Separate queries into a separate config file • Segment->Feature->SubFeature • [GENERAL] • description = PlasmoDB Release 5.3 • db_adaptor = DAS::GUS • database = dbi:Oracle:sid=crypto;host=rad.rcc.uga.edu;port=1521 • user = gususer • pass = pass • db_args = -sqlfile =>$ENV{DOC_ROOT}.'/gbrowse.conf/plasmodb.xml'

  5. features segment

  6. PBrowse

  7. Synteny Browser - SynView Steve Fisher will present it in details later

  8. Track Customization

  9. init_code = sub hover { use HTML::Template; my ($name, $data) = @_; my $tmpl = HTML::Template=>new(filename=>$ENV{ROOT}.'/gbrowse/hover.tmpl'); $tmpl->param(DATA => [ map {{@$_ > 1 ? (KEY=>$_->[0], VALUE => $_->[1]):(SINGLE => $_->[0])}} @$data]); my $str = $tmpl->output; $str =~ s/'/\\'/g; return qq{" onMouseOver="$cmd;return escape('$str')}; } link_target = sub { my $f = shift; my $name = $f->name; my $start = $f->start; my $stop = $f->stop; my ($freq) = $f->get_tag_values('RawCount'); my ($tag) = $f->get_tag_values('Sequence'); my @data; push @data, [ 'Location:' => "$start..$stop" ]; push @data, [ 'Sequence:' => $tag ]; push @data, [ 'Library:' => $lib ]; push @data, [ 'Frequency:' => $freq]; return hover( "Sage Tag - Temp ID $name", \@data); }

  10. Future Works • Performance tuning – SQL, bulksubfeatures, AJAX tooltips • Unification with web inferface WDK • All projects share same gbrowse configuration • Be able to divide the .conf and .xml files into sub files • Be able to include/exclude based on project • Re-using sql and perl across tracks, e.g. duplicate code

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