GBROWSE TUTORIAL
Lincoln Stein
May 7, 2003

This is a quick tutorial to take you through the main features and
gotchas of gbrowse.  This tutorial assumes that you have successfully
setup MySQL, Perl, GD, BioPerl and the other gbrowse dependencies, and
that you have successfully loaded and browsed the yeast test data.

We will be working with simulated Volvox genome annotation data.  The
database will be named "volvox" and gbrowse will be invoked with this
URL:

  http://your.host/cgi-bin/gbrowse/volvox

1.  THE BASICS

The first step is to set up a new database named "volvox."  Using the
mysql tool, create the database, grant yourself read/write privileges,
and grant the "nobody" user read privileges:

  % mysqladmin -uroot -p create volvox
  Enter password: *********

  mysql> create database volvox;
  Query OK, 1 row affected (0.04 sec)

  mysql> grant all privileges on volvox.* to lstein@localhost;
  Query OK, 0 rows affected (0.00 sec)

  mysql> grant select on volvox.* to nobody@localhost;
  Query OK, 0 rows affected (0.00 sec)

  mysql> quit
  Bye

Replace "lstein" with your own login name.

Now load some sample data.  In the "data_files" subdirectory of this
tutorial you will find the file volvox1.gff.  This contains a series
of 15 simulated features

% fast_load_gff.pl -d volvox -c volvox1.gff 
Fast loading enabled
SUCCESS: 16 features successfully loaded

See volvox.conf for baseline configuration

----------------

2) ADDING NEW FEATURE TYPE

% ./random_feature.pl motif Motif m > volvox2.gff
Load this file.

Add this to config file

[Motif]
feature      = motif:example
glyph        = generic
bgcolor      = blue
height       = 6
stranded     = 1
description  = 1
key          = Motifs

----------------

3) ADDING NOTES

See volvox3.gff

4) ADDING SEGMENTED FEATURES

See volvox4.gff

config:

[Match]
feature      = alignment:example
glyph        = segments
bgcolor      = orange
connector    = solid
height       = 6
description  = 1
key          = Matches

5) MAKING OWN AGGREGATOR

See volvox 5.gff.

aggregators = transcript alignment orf MySkipper{skipper}

[MySkipper]
feature      = MySkipper:example
glyph        = segments
bgcolor      = red
connector    = solid
height       = 6
description  = 1
key          = MySkipper

6) avoiding loss of unmapped segments

See volvox6.gff

aggregators = transcript alignment orf MySkipper{skipper/skipper_whole}

7) Making things that look like genes

[MySkipper]
feature      = MySkipper:example
glyph        = transcript
bgcolor      = red
height       = 12
description  = 1
key          = MySkipper

8) Semantic zooming

[MySkipper:20000]
feature      = skipper_whole:example
glyph        = generic
stranded     = 1
bgcolor      = red
height       = 12
description  = 1
key          = MySkipper

9) Placing something in the overview

[MySkipper:overview]
feature      = skipper_whole:example
glyph        = generic
stranded     = 1
bgcolor      = red
height       = 3
description  = 1
key          = skippers

10) canonical gene

See volvox7.gff

aggregators = wormbase_gene alignment orf MySkipper{skipper/skipper_whole} 

[Genes]
feature      = transcript:example
glyph        = wormbase_transcript
forwardcolor = violet
reversecolor = indianred
utr_color    = gray
bgcolor      = red
height       = 20
description  = 1
key          = genes