Our Task At Hand Aggregate data from every group

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Charles Harmon
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1 Where magical things happen

2 Our Task At Hand Aggregate data from every group That s not too bad? Make it accessible to the public Just some basic HTML? Simple enough, right?

3 Our Real Task Manage 1 million+ records in the database ~275k per strain, and this number will grow Present your data in a sensible manner We don t want to lose the user The finished product has to be functional

4 Required Features Functional Genome Browser GBrowse Some form of a details page Ability to Blast against strains Make it look good

5 The Game Plan Divide the group into subgroups Database Management GBrowse Pathway-Tools Just hack away, simple as that.

6 Something New GFF3 and Bio:SeqFeature New schema more appropriate to GBrowse2 A lot of code written from scratch PHP, JavaScript, SQL, not so much Perl Documentation To give future groups a head start

7 GFF3 and its wonders

8 General Feature Format 3 (GFF3) Extension of the Sanger GFF2 format Has bioinformaticists in mind = split(/\t/, $gff_line);

9 GFF2 vsgff3 Sample GFF2 data Sample GFF3 Data

10 GFF3 Layout Column 1 seqid Column 2 source Column 3 type Column 4 start Column 5 stop Column 6 score Column 7 strand Column 8 phase Column 9 attribute

11 Start, Stop and Strand Trap Often lost in the results Lost in InterPro, CDD, some Blast outputs Predictions GFF3 files aid in recovery Watch out for amino acid starts and stops!

12 The Attribute Column Complete freedom Not sure where to put it? Custom tags Examples: blastpg_acc, member_db, interpro_acc

13 The backbone of everything

14 GFF3 Column 9 Name of Gene Source of Gene Species/Strain Parent/Consensus Children interpro result - blast PG - CDD Function/GO terms tables and 6 Databases - A combined database for all strains - Perl Module is used to populate the database

15 Database Schema

16 Gene Name Gene ID-parent /children consensus gene_prediction srna:rfam trna:trnascan-se CDS:BlastPG misc_feature:cdd misc_feature:interproscan Evalue CDD type blastpg Interpro_acc

17 A magical Perl creation

18 Overview GBrowseis a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Simultaneous bird's eye and detailed views of the genome. Scroll, zoom, center. Use a variety of premade glyphsor create your own. Attach arbitrary URLs to any annotation. Order and appearance of tracks are customizable by administrator and end-user. Search by annotation ID, name, or comment. Supports third party annotation using GFF formats. Settings persist across sessions. DNA and GFFdumps. Connectivity to different databases.

19 Installation Dependency Apache HTTPD web server, PHP, MySQL # sudo yum -y install httpd php mysql mysql-server php-mysql Perl modules dependency # sudoyum install perl-cpan Installation # perl Makefile.PL CONF=./gbrowse_conf HTDOCS=./gbrowse2/ CGIBIN=.html/cgi-bin 'CONF' is equal to where you want the config files to stored 'HTDOCS' is equal to the directory you want the html files to be placed 'CGI-BIN' is equal to the directory you want the GBrowsecgi files to be saved Install the missing perl modules reported by perl Makefile.PL # make # make install

20 Setup Global configuration Gbrowse.conf User conf files Example Create one track to display predicted genes from two resources (Glimmer and GeneMark) Different colors Descriptions, naming, and

21 GFF3 data

22 Step 1: Add the user conf file Edit the main Gbrowse.conf, and add this stanza to the bottom of the file: [Mtest] description = Example path = /YOURPATH/ example.conf Create the example.conf [predicted_genes:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor memory -dir /YOURPATH/data

23 Step 2: Add customized track Add this stanza to the config file [Genes] feature = gene glyph = gene database = predicted_genes bgcolor = sub { height = 6 description = 1 key = Predicted gene my $feature = shift; = $feature->notes; = $feature->attributes('name_source'); If ($note[0] =~ /Glimmer/) { return red';} else { return purple';}

25 Lisp on steroids

26 Pathway-Tools Web Server Multiple User access Comparative genomics tools are available to generate summary tables comparing metabolic networks across a user-specified set of PGDBs. An Advanced query tool, allows users to formulate precise queries through an interactive form. Customize pathway diagrams for PowerPoint or publications. BLAST searching allows the user to query a desired sequence against an organism's complete genome.

34 Questions and Comments Specific features? How did we do this or that? Help with GFF3? Etc

Chen lab workshop. Christian Frech

Chen lab workshop. Christian Frech GBrowse Generic genome browser Chen lab workshop Christian Frech January 18, 2010 1 A generic genome browser why do we need it? Genome databases have similar requirements View DNA sequence and its associated